I liked a lot of the ideas in the ending. You have the desperate charge towards the transport beam, dodging Reaper blasts and only just making it in while the rest of the army is wiped out and you and Anderson are the only ones to make it through with criticial injuries. Then you have the confrontation with the Illusive Man, which was tense and well-acted, even if it was just Saren 2.0.
He and Anderson die, (no shortage of tears there), Shepard opens the Citadel arms, and is about ready to join them when Hackett calls. Then you get to meet the creator of the Reapers, learn about their motivations, and make a choice between three morally grey options that will end the Reaper cycle and essentially change the entire galaxy. What's not to love about that ending?
Well, obviously the execution. All of these ideas are good, they were just presented poorly. Things start bad by giving the creator of the Reapers the voice and appearance of an eight-year old boy, making him impossible to take seriously. The whole place felt too much like a dream seuqence, which has resulted in a whole bunch of half-baked fan theories that this wasn't the proper ending and that Shepard was in an indoctrination-induced coma for the whole time. Which would be a far worse ending than what we got, since it means the game was incomplete and that Reapers are technically still winning the war.
While the choices were all inheritly different and morally grey, all we got to see was one cutscene with different colour filters depending on what you picked with no proper aftermath or closure. Seeing the Normandy crash on the garden planet was actually pretty nice (I was glad to see Garrus alive, since I thought he'd died in the final push), but then you realise that with no Mass Relays, they have little hope of rescue and could very well end up starving to death. All in all, it came across as bleak, unexpected and anti-climatic.
TL;DR - Good ideas, poor execution. But hey, there's always EC.