I think a lot of people (myself included) jumped on the 'the ending sucks' bandwagon before they ever actually played it. Once I beat the game myself, I didn't mind it at all. I think people just wanted an ideal "Everything is great, you saved the day, married your sweetheart, and are now Space King" ending, and were gutted when they didn't get it.
If you read about the theory that during the entire final mission, Shepard was actually indoctrinated, then it's actually an incredible ending.
I've read up on that theory and I don't think it's the case for one of a few reasons, one of them being that indoctrination is a slow process unless you are a machine like the geth and there are also a few warning signs that go with it too, I think TIM was indoctrinated but Shepard not so much.
now with that being said if it is that shepherd is indoctrinated at the end of the game 1, the ending goes to holy fuging bat poo batman awesome, and 2 I hate it all at the same time.
i'm personally fine with a ending that Shepard does not survive as long as he saves the rest of the galaxy while doing it, but one thing that I did not like about the game is the total lack of choice that you had over how the story ended, which is something that has been a staple in all the mass effect games have been all about the choices you make, Like in ME1, you saving the council and also deciding who the new councilor for earth would be, in mass effect 2 the choices were too many to count almost, but in the 3rd you basically had one choice or out come to the game and if you did not like it tough luck