The biggest problem about ME3's ending is that they tried to pull the curtain back on the Reapers' motivations. There was really no need to do that. The strength of the core narrative and themes of ME3 was enough to invest players through to the end. The Reapers could have just been intergalactic bogeymen and it would've been just fine.
If one wants to argue that point, then I would bring up an irrefutable one about how poorly Bioware handled the Reapers' backstory. If they wanted to tell us all about the Reapers, the one way that you SHOULDN'T go about it is to introduce a new character in the final 10 minutes to deliver the giant info-dump. They had a whole game to drop hints about what the Reapers are, but instead they split the focus and made Cerberus the major antagonist for much of the game.
It's poor writing, even if we were to disregard the actual contents of the writing.
BOOM
I think thats a very good point.
It is still my favorite series ever as a whole (and I don't despise the ending either really) but at no point in playing it did I ever think, 'I better find out why the Reapers are here!' while I was playing.
Honestly I thought Mass Effect 1 explained more than enough there. They were the gods of the universe come to harvest and clean when they saw fit. Somethings are bigger than any tiny mind can understand.
I can't remember the exact dialogue but Soverign says something to you like, "we have no beginning, we have no end, we simply are"
And then you being a tiny stubborn human decides to take it upon yourself to try and kill god.
Thats all I wanted or needed to know....
And even if they did feel the need to explain more, it should have been seeded throughout the games, or at the very least the 3rd game.