Still liking the game despite using some helpful mods. I think I finally reached level 46 though. Barely got most of the top of the map cleared out now. Only a few places I can't get to because they require specific quests to be active to enter them. At this rate it is going to take me a few more months at least to finish the game.
As far as build and perks go, here is my take.
S.P.E.C.I.A.L.
Strength = Unless doing melee you can leave this at 3 or less at the start of the game. If doing melee needs to be 5 or higher. The only useful perks under this tree for non melee types is strong back and armor smith. You can get by without armor smith for most of the game and strong back as well. Strong back is a nice convenience perk, but definitely not required. Steady aim is great if you are going the automatic rifle setup, but seeing as that and melee are sort of subpar setups in this game, I wouldn't bother too much.
Perception = fairly mandatory for shooters. Starting with a 4+ is highly recommended. This gives you access to at least the locksmith perk from the start of the game.
Endurance = Unless playing melee can keep this as a dump as well. I will say that if you want to start with this at 5, gaining the Aquaboy/girl perk from the get go is great!
Charisma = Makes doing many quests easier by far. Not exactly required, but some quests will be hard pressed to be completed without having this high. Also helps immensely if doing any form of settlement building. Also the intimidation perks are pretty darn good perks in this game. This stat massively affects prices at merchants for both buying and selling. Lone wanderer is a perk that really shines once you are done with all companions or just hate using any companions. Although you can still use dogmeat with the perk.
Intelligence = Like most previous Fallout's this is a highly useful stat. While previous Fallouts this was a required to be high at the beginning stat (or maxed in some previous games for good min/maxing) FO4 allows you to actually play a dumb character if you want and get away with it. If you go the idiot savant route you will level up much faster than others which allows you access to perks for other stuff before you finally focus on leveling intelligence. The problem is lack of gun nut, hacker, and science. 3 very good and almost essential perk trees, which require an Int score of 5 to get. Also higher Int helps with some Institute and Railroad quests.
Agility = Another highly required stat. If not the most important stat in FO4. Required to be high for both melee or non melee characters Really should be 5+ from the get go for most players. Lots of really good perks in this tree.
Luck = Good tree, but can be lower for starting out. Each point increases amount of caps and ammo found though and allows for more crits while playing in both vats and outside of vats combat. Unlike previous Fallout games, luck is much more useful in FO4 at least.
Now for perks list and what I feel is good/bad
Strength Perks
Iron Fist: good if going claw melee build I guess. Otherwise it's a waste. Still with the right build this can dish out pretty good damage late game. It just means you suck most of the game though. No need to worry about ammo though.
Big Leagues: if doing melee this is a bread and butter perk. If not skip it.
Armorer: A perk that is good for every build. For melee taking this soon can help a bunch, but it should still be maxed out later by even shooter builds.
Blacksmith: useful only to melee builds
Heavy Gunner Very sub par perk. Not many guns in FO4 use this perk. Those that do use this perk, you rarely find ammo for in the game. Of the heavy guns, fatman basically 1 shot kills everything in the game if you land a direct hit. The flamer and mini guns use way too much ammo for their damage. Although a minigun with the legendary explosive mod can wreck just about anything, it is still more a fun novelty use than anything else. Definitely more for a late game build once ammo for the heavy guns isn't as big of a concern.
Strong Back: Nice for the convenience, but not a necessity. One can always mod or use console commands to render this perk completely useless too.
Steady aim: Mostly useful for automatic guns. Which are mostly subpar guns as well. Although it's not bad for pistols either. Still the strength requirements for gunners make this a very late game pickup if picked up at all.
Basher: Because you don't want to backpedal and shoot instead I guess. Mostly a worthless perk. If you want to go melee go melee. Almost no need for this perk at all for shooters or melee.
Rooted: This is an OK perk. Still, it's better to move and not be hit, than stand still and take damage even if it is reduced damage. The extra ranks in this perk are more melee focused though.
Pain Train WOO WOO!!! Ok, this is a good perk if you like using power armor a lot and are a melee build. It is pretty darn useful then. Otherwise, it's bleh.
Perception
Pickpocket: minimal usage. Not many people have much you can pick pocket off them unless you spend many ranks on this skill. It is fun to disengage from a raider in power armor so you can sneak around back to pickpocket their fusion core. Which automatically pops them out of the armor. Otherwise it's not an essential skill unless you really just like being the asshole.
Rifleman If you aren't melee or pistol only, then get this perk. More ranks is more damage. This affects lasers and ballistic rifles.
Awareness only has 1 rank and it's darn useful. Get it for all builds.
Locksmith highly useful as master locks come far before master computers. While Cait can pick master locks, you find her later than Nick Valentine who can hack master computers about when you start encountering them more. Highly recommend getting 3 ranks in this.The 4th rank isn't really needed at all though unless you really suck at the mini game.
Demolition expert: Good skill, but not required from the start. Allows crafting of explosives and makes anything that goes boom really go BOOM! Still, for the most part the damage from most explosive even without this perk tends to 1 shot stuff that isn't legendary. So I wouldn't put points into this early.
Night person: BLeh. If you like to think of yourself as a vampire I guess. But mostly crap.
Refactor Any form of damage resistance is nice. Although early on you won't run into many energy based damage guns. Although around 20 you will. Still it's easier to rank up armor to cover than before putting points here. Do get eventually.
Sniper The first rank is excellent. The next two are ok.
Penetrator fun fluff. Overall nothing to be too excited about.
Concetrated fire Decent capstone perk. although usually by the time you reach 10 perception with some perception gear, the ranks in this aren't as great as they would have been when you had lower perception. I wouldn't race to get this though, but I do recommend getting it.
Endurance
Toughness Nice first level perk. Useful for all builds and required early to get a few ranks for melee builds if not race to max for melee builds. Shooters can hold off though.
Lead Belly Bleh. Not worth. Healing through stems, purified water, and beds is way too easy to waste time with rad crap.
Lifegiver good for melee as you'll take damage more often so the extra life helps a bunch. For shooter it is also nice, but nothing to race for.
Chem resistant Bleh. If doing a melee chem build, which chems help melee builds more than shooters, this is sort of useful. So if you plan to use chems with a melee build then it's decent.
Aquaperson Get 1 rank at least regardless of your build. No more rad damage from putting your toes in water or even going completely under. Seriously good perk. Second rank is nice, but not required.
Rad Resistant It's okay, but not really required since you can get the Hazmat suit. Plus power armor and provides a nice amount of rad resistance. Also it doesn't work well with the Ghoulish perk as they counteract each other if you plan to get the Ghoulish perk. Also, rad-x stacks.... so the +30 rad resistance you get at max rank from this perk is bleh over all.
Adamantium Skeleton Surprisingly useful! More so if you aren't the type of person that reloads the game everytime you screw up and step on a landmine. Still, nothing to race for usually.
Cannibal If you don't plan on having any followers but dogmeat or Strong then you can actually use this perk. But since healing is so easy other ways, it is a straight up RP reason to even consider taking this. Also taking this seems to automatically make some charisma checks harder.
Ghoulish Decent perk overall. It doesn't stop you from taking rad damage though. Late game feral ghouls aren't as big of a problem either. Still, other ways to heal, and not needed.
Solar Powered Bleh. Don't bother
Charisma
Cap Collector Very nice but certainly more of an end game perk. You don't be buying and selling much early game so I wouldn't put points into until much later.
Lady/Man killer Decent I guess. The most enemies in this game tend to be raiders which tend to be human. Still, I don't consider this as powerful as it was in previous games in the fallout series. Can be skipped.
Lone Wanderer Great for stealth builds that go solo or with dog meat(since dog meat doesn't count as a companion). Adds a ton of damage to your build as well as carry weight if you require that. Even if you do use companions early on, chances are you'll blow through them all eventually and just stick with dog meat at most. Making this a perk to eventually pick up regardless of playstyle.
Attack Dog Like Lonewanderer. Decent with dogmeat, not needed if you don't use the dog. I wouldn't race to rank this one up although 1 rank near the start of the game in this can be very useful as dogmeat is the first friend you find.
Animal Friend OK skill overall. Can be picked up later though in most builds unless doing a pacifist run. Still, there aren't that many aggressive animals that are that troublesome in the game. Molerats and mongrel dogs mostly.
Local Leader Required eventually for settlement building. Otherwise can be skipped until late game. If you really hate the settlement building mini game this is a worthless perk then.
Party person If doing the chem doping melee build then sure. Otherwise why bother?
Inspirational decent, but not required. Most of the time your companion, even with a gun, is stupid. They can't die so accidentally shooting them isn't a big deal. They tend to run out first so chances of being shot by a companion is very remote. Since they run forward to die most of the time, the added bonus damage for them is almost pointless. Still, it can help in some fights. I wouldn't race to max this though unless you really are hurting to have your companion carry a tiny bit more weight.
Wasteland Whisperer Like animal friend perk and the intimidation perk, this is an OK perk. This perk is better than Animal Friend at least as there is more stuff to pacify with it at later levels. It is also more useful if doing a pacifist run/build. The problem with all these 3 perks is most enemies spawn at or above your level when you first encounter them. Which makes the perk useful if you are backtracking areas where stuff that spawned stays spawned lower level than you (assuming you left the spawns untouched).
Intimidation Like Animal Friend and Wasteland Whisperer. This affects humans where as the other two affect either animals or creatures. Since there are more humans in the game, this is slightly more useful than the other two perks.
Intelligence
VANS waste of a perk. Just look at your mini map and compass more.
Medic Very useful perk for any build. Stimpacks and rad-aways are your lifeblood in this game and the more effective they are then the more effective you are. For melee builds this is essential to get maxed early. For others get a rank as needed.
Gun Nut Max ASAP, unless of course you are melee build. It makes everything you shoot better. It works with settlement defenses too.
Hacker Hack harder computers. Eventually get 3 ranks, but you can rely on Nick Valentine if you prefer. Master computers show up much later in game and aren't as proliferate as locks so this isn't a must have race to max like lockpicking
Scrapper Very nice perk once you start breaking down stuff. Still, you can just store most stuff in your workshop until you are ready to break stuff down and make use of this perk. So no need to max this early. Also, it basically only lets you scrap the "mods" on stuff into their base components. If you scrap an un modded gun or armor piece you'll only get leather or steel.
Science! Very useful perk to get. Allows better scopes modding of energy weapons, making several settlement items, some armor mods, and useful for some quests in the game.
Chemist Uhhh, unless playing a chem addicted melee build this can be skipped. Even for chem melee builds, this is a lot of investment into the intelligence tree.
Robotics expert Somewhat useful. Not that many robots to hack though. Is used for some quests though.
Nuclear Physicist Great if you love to use power armor! The gamma guns are decent late game as well to anything that isn't resistant to them like ghouls.
Nerd Rage! No.. just no.
Agility
Gunslinger If focusing on pistols this is a must have. If focusing on rifles/shotguns then this isn't as useful to max early. Still pistols are great to use in this game.
Commando since automatic guns in this game are subpar, this perk is also subpar. Only get if you really want to use automatic weapons and don't have any ammo problems because you cheat or use the mod that allows you to craft ammo.
Sneak Unless you have a problem with min/maxing get this skill for at least 1 rank. While not required to max, it does make the game easier.
Mister Sandman if you going around sneaking and shooting people then get this perk too. More damage is always nice.
Action Person Another very nice perk unless you are one of those people that refuses to use the VATS system. Which in Fallout 4 is doable at least since regular shooting works well now. So while not required, it's definitely nice to rank up when you can.
Moving Target Its okay. Moving makes you harder to hit anyhow, and if you are sneaking + shooting people this perk will rarely ever make a difference. So I wouldn't bother getting this early in the game unless playing a melee build.
Ninja Nice for those that sneak around to kill stuff. Max fairly soon if you do the sneaking playstyle
Quick Hands decent perk, but not game changing. Less so if you use a weapon with the Neverending ammo legendary mod. Can be skipped until late game.
Blitz good for melee, skip for the everyone else.
Gun fu a decent capstone skill for once. Although not game changing. Can wait for awhile to max out and you probably won't have access to it early on anyhow.
Luck
Fortune Finder Nice perk for at least 1 rank early on. Still, you won't tend to buy much off vendors early, and ranks in charisma will save you more overall than ranks in this.
Scrounger Nice perk as well for finding more ammo. If playing vanilla without the ammo crafting mods this helps a bunch for any shooter player. Required if doing an automatic shooting playstyle. Melee builds can skip.
Bloody Mess More damage and more gore WHOOPEE! Get it.
Mysterious stranger Required if doing pacifist build. Otherwise can be skipped unless you like random stuff.
Idiot Savant Required if playing the idiot build. Otherwise skip.
Better Criticals Get it and max it when you can. Although my build doesn't start luck out high enough to get this all that soon.
Critical Banker fun but can be skipped
Grim Reapers Spirit another fun perk, but can be skipped.
Four Leaf Clover same. Fun but skippable. I will say that while Spirit plus Clover are chance based; when they go off a lot then you can chain crit hits together when you also have Better Criticals and Critical Banker in the VATS system to devastating effect. But you need to chain the effects which is all random chance, and requires you to be engaged in a battle with a ton of enemies surrounding you. Of which that is rare position to find yourself in unless playing dumb.
Ricochet another fun but skippable. These last three perks do make the game easier, but aren't really required for any build. However, this is more useful if doing a pacifist build at least and almost required for that build.
So there my break down on stats and perks. For min maxing, this is how I would do it. First my SPECIAL stats at the start. This is how I would distribute the initial 28 points
S = 1
P = 7
E = 5
C = 3
I = 6
A = 5
L = 1
Then what I would do for the first 41 levels. I go for maxing perception first since that is the first bobblehead and this way you'll have 11 perception. That and it affects VATS accuracy which helps a ton.
For reference, with some charisma gear on, you can pass most low level charisma checks in the game with a 3 starting charisma. Add in a clean suit for +2, glasses for +1, and formal hat for +1 for a 7 charisma to pass checks with.
1 - Aquaperson (yes start with this)
2 - Lockpicking
3 - Gun Nut
4 - Sneak
5 - Rifleman
6 - Awareness
7 - Lockpicking (rank 2)
8 - Scrounger
9 - Medic
10 - Science
11 - Mister Sandman
12 - Rifleman (rank 2)
13 - Gun Nut (rank 2)
14 - Hacker
15 - Perception (rank 8)
16 - Sniper
17 - Mister Sandman (rank 2)
18 - Rifleman (rank 3)
19 - Locksmith (rank 3)
20 - Science! (rank 2)
21 - Hacker (rank 3)
22 - Perception (rank 9)
23 - Perception (rank 10)
24 - Agility (rank 6)
25 - Gun Nut (rank 3)
26 - Agility (rank 7)
27 - Ninja
28 - Science! (rank 3)
29 - Ninja (rank 2)
30 - Mister Sandman (rank 3)
31 - Rifleman (rank 4)
32 - Strength (rank 2)
33 - Strength (rank 3)
34 - Armorer (rank 1)
35 - Armorer (rank 2)
36 - Armorer (rank 3)
37 - Ninja (rank 3)
38 - Luck (rank 2)
39 - Gun Nut (rank 4)
40 - Armorer (rank 4)
41 - Science! (rank 4)
That's the basic build I am doing. There are several reasons. I am maximizing damage from sneaking + long guns. I tend to use rifles + shotguns when I can (or pistols when out of shotgun ammo). I do carry around a fatman for deathclaws (especially the legendary ones). This build gets all the crafting maxed ASAP. After 41 one can bump charisma up for better questing and settlements, or luck to get Bloody Mess for more damage, and then start maxing stats. Currently with the build I am doing I am going for luck rank 3 and then bloody mess for max dps. Get the last rank of rifleman at 46 with my build though, and that about tops out the damage with a maxed Mister Sandman and Ninja already. Further ranks of sneak are nice as well as ranks of medic if you are having problems. I have found I don't have much problems though with 1 level of sneak and 1 level of medic.
Stat wise for leveling after 41 I consider the stats in the following order of priority. Charisma, Agility, Luck, Endurance, and finally Strength. Try not to pick up the corresponding bobble head for the associated stat until it reaches rank 10 in that stat. Otherwise you can't get it to rank 11 if you want to truly min/max.
I am currently level 46, as stated previously, and liking the build. I explored about 1/4 of the map (maybe that much) when I check out the online maps for the game versus what I've done. I haven't even touch most of the faction quests, only the first few for Minutemen and Brotherhood of Steel. I doubt I'll ever max the character out completely though. despite how far I've leveled in comparison to how much of the game I've completed.
I hardly buy or sell anything in the game and usually scrap everything or reuse what I can. I only use VATS when I need to hit a specific spot on a target running at met like a feral ghoul to blow a leg off. That's why the high perception is key for those moments you just can't stay sneaky and snipe. Then you need to backpedal and hit spots before swapping to a shotgun and aiming in the general direction of the target's face to finish them.
I did use the console to screw around with all the perks though to try them out and fine tune my build so I could bring you guys this list.