...Sigh.
The ending of ME3 is not a "small" problem. The writing has always been Mass Effect's strength. The story, the characters, the lore, are all well-written and I think it's safe to say that almost anyone who calls themselves a fan are, primarily, fans of the writing first.
So the ending of this trilogy takes all of that good writing, and essentially undoes it. It screws with the writing of the main character, making him/her act contrary to who he/she always was regardless of morality (by which I mean, determined and unwilling to lie down and let crap just happen). It screws with the writing of the actual lore. And the writing, in and of itself, is BAD. Any writer, presented with the ideas outside of context, and agree that it probably wouldn't work. You don't add new characters, new rules, new lore, etc which will totally change the way things work in the last few minutes of the final part of a series. It's bad writing, no matter what media is being written.
So the main strength of the series and the thing that most fans are fans of is completely turned on it's own head and bounced against the concrete for a bit.
And that strength is the sort of strength that stays with a person. Good game play is fun for a while, then you put the game down and go off to do other stuff and it doesn't haunt you. Good writing can. There are powerful books which can stay with a person for their entire life because of the way it's written. Same with movies. Writing is something that can get into your head, stimulate your emotions, make you think and feel, and because that's the strength of the Mass Effect series, it succeeded. It got into peoples' heads. Maybe not YOUR head, but don't discount the power strong writing can have just because it's not impacting you personally.
So combine the combination of the generally good writing, and the fact that that has the potential to get in people's heads, to stay with them and leave lasting impressions; with the magnitude of really, REALLY bad writing in the ending, in all areas across the board... That's why it's a big problem. That's why it's causing so much uproar.
I'm not going to include my thoughts on the ending, or why I think them, or my thoughts on the fan response here. This is simply a post on WHY the fans responded as they did.