The endings stank because 1) All your previous decisions from ME1, ME2, and ME3 are meaningless. They don't impact the endings you get at all. 2) In the original cut ending, all three endings resulted in a dead Sheppard and a completely destroyed galaxy. Only partially resolved in the extended cut ending. 3) The Star Child that shows up at the end, explains everything and removes all the mystique from the reapers, introducing a new character in the last 10 minutes of any story solely to wrap it up is piss poor story telling. 4) The massive plot holes, more in the original cut, but they still exist in the extended cut. Things that Sheppard, regardless of your decisions and play style, would never do. 5) You don't get a shred of closure on any of your squad members or romance choice. 6) The final slap in the face, at least, to me, the prompt to go buy more DLC after ME3's credits roll.
It's the lesser of two evils in terms of implementation. They make a difference to your 'war assets' which directly influence your ending possibilities; and pretty much every decision you make alters both small and big things along the way as well. But the other option is to make them a binary switch where "If you didn't save the Rachni, then XYZ" and "If you didn't save the Council, then ABC" and so on and so forth. The problem with that is as soon as players find out they don't like what their choices do they're going to complain even more that they'd have to go all the way back to/through ME1 and ME2 to change it. Further the more weight you give those decisions, the more you take away from someone who just played ME3 or lost their saves or switched consoles/etc. Ultimately I think by making them contribute to your aggregate rather than making them "yes/no" was the right call.
Destroyed how? If you control the reapers or synthesize with them (which as the catalyst says grants the galaxy the collected knowledge, experiences, culture and more from the harvested civilizations through their reaper proxies) the galaxy is on the brink of being greater than it's ever been. And that much is evident/implied without the extended cut, all that does is basically visualize it. Shep's death is not a non issue, but relative to the galaxy's future, it's minor. I think it's appropriate, Shep's role through each game has been as the galaxy's protectorate; I think whether or not he/she would make the ultimate sacrifice is no question.
3, imo
Aside from some questions of lore I can't really think of any major holes at least. Though as Paragon Shep I kind of 'played the part' the whole time, maybe if you were Renegade you'd feel differently about certain actions, but I don't know which.
5 is true without the extension, but at the same time that's a touchy subject given people's attachment to certain crewmembers. I think at least seeing them make it out ok is appropriate (which the extension did) but going much past that would encroach on player's imagination of what comes next for each crewmate, particularly with regards to the romance.
Didn't watch the credits, couldn't say. I did have From the Ashes and the extended cut installed when I beat the game but didn't notice anything saying as much at least.