Parts of the ending that a lot of people fuss about make sense.
[spoiler]The mass relays were Reaper tech left behind to make everyone develop how they wanted. The relays had to go if the galaxy was to be completely free of their control.
"The Shepard" having a Jesus ending was something that could be seen coming from all the way back in the first one. And, my Shepard deserved some peace; she was living on borrowed time after the Collectors already killed her. She gets to relax and wait for Garrus at the bar while watching baby krogans.[/spoiler]
Other parts, um... not so much.
[spoiler]Silly Reapers, did you not notice EDI and the geth fighting you to save organics?
Annnnnnd, why was the Normandy in mass relay flight when we were fighting for Earth until the last second?
Joker saw Space Magic coming and thought "No, I'm not going to be part of that mysterious space mystery stuff, and neither are my friends!", so he took your squadmates and tried to escape.
[/spoiler]
I don't hate the ending,
[spoiler]A broken and exhausted Shepard climbing to her feet as she asks, "What do you need me to do?", summed the character up so well.[/spoiler]
and I don't like it.
[spoiler]After everything else, it felt out of place and tacked on. Sovereign's unfathomable to puny organic minds motivation turns out to be a bad case of "what if" with the synthetics in the game doing the exact opposite. ALL AI will wipe out organic life in the galaxy, hmm? Reapers sound like racists~[/spoiler]
But, I don't think it was enough to make me rawr at the game or the series.
[spoiler]Mordin singing when he cured the genophage because someone else might have gotten it wrong
Legion saying "I"
Thane's last prayer being for Shepard
The quarians having a home again
The lady with Alzheimer's looking for her son
The asari with PTSD
[spoiler]And the horrible realization the girl she killed was Joker's sister[/spoiler]
Jack with her biotic ducklings
Anything Garrus
Anything Wrex "It's time for krogan to do what we do best: saving the galaxy from giant monsters."[/spoiler]
Those bits and others make up for it.