Alright, for simplicity I'll refer to Imperium Galactica 2 as IG2, and Galactic Civilizations 2 as GC2.
GC2 has 3D combat but it doesnt look quite as good as IG2. It also wont let you issue any commands. You just have to wait it out. You do have complete control over battle speed and viewing angle though.
GC2 lets you completely cutomize ships even down to trim pieces that have no practical use. However, like IG2 you dont really need to make tough decisions because you will always want to put on the "best" weapons and armor: items that give you the most points while taking up the least space. Also, there are no real "special" modules to put on ships. However, you do have to decide how many (if any) points you want to put into mass driver weapons, energy beams or missles. Conversely, you need to decide how much armor, shields or point defense you want, if any. So you do have to make some decisions when building ships, but its not quite as details or brain-intensive as Moo2, where you had a buttload of weapons and any of them could be upgraded in 4 or 5 ways.
Also, in GC2 you can choose to spend as much space as you want on engines. You can vary your speed between 1 and almost 100 (I think) depending on how much space you have available and your tech level of engines. All this put togther has the distinc advantage of letting you add speed, weapons and armor to your colony, construction and transport ships.
In GC2 you can have some planetary defenses but its not as involved as IG2 or Moo2. Also, unlike IG2 you dont build battlestations right around your planets. You put them out in space. You can have as many as you want but it makes sense to build fewer of them and then upgrade. Every time you fly another constructor out to a base you can give it a new module. When you advance technology far enough I think you can have around 75 modules on one base.
You can have three different types of bases. Influence, Military and Trade. All of them let you add weapon and defense modules, but the military ones also improve the stats of nearby ships. If you can get the radius high enough and add enough Assist modules you can improve a light fighter with 2 points of energy damage and no armor and turn it into a powerhouse with 20 points of all weapons and 10 points in all defenses, just for being nearby.
One last note, instead of building one of every type of planet improvement (like in Moo) you have multiple build zones across each planet that can have whatever you like (similar to Ascendancy). They can also be upgraded when your technology improves (similar to IG2). Some zones are useless until terraformed. Some do better if you put a certain type of building in them like research or manufacturing. Also, farms are helpful, but not absolutely required in this game. Food only increases your max population and I dont think people can actually starve.
As for planet invasion, you have limited control like in Moo2, you just send a bunch of transports to a planet and maybe issue a general strategy then sit back and watch. No tank games like IG2. You are not able to sit off-world and bombard with ships either. They can only attack other ships in orbit.