I feel these days like the ending was just the tip of the iceberg of a colossal mess and horrible game. But, besides that, I'll just do my usual thing about the ending.
When I had first heard the complaints of the ending, I was actually expecting to be happy with it because people tend to hate things I like. For example, I loved Dragon Age 2 and really loved it's ending. However, to me the ending of Mass Effect 3 simply makes no sense when you look at the themes of the rest of the game. Synthetics vs Organics was just a small issue apart of the much larger issue of everyone learning to tolerate each others differences.
Reapers, husks, collectors, are synthesized beings, organics mixed with synthetics, and they are presented as horrible and unwanted. Not something to ever be desired.
Pure synthetics are presented as innocent victims of organics. Organics are the ones that abuse, try to control and destroy synthetics, not the other way around. Legion, the geth, and EDI all want to be organics friends and live in peace. Any attacks by them against organics are either in defense, through pure misunderstanding, or in the case of the geth in ME1, they were reprogrammed/manipulated by Reapers and Saren. You can fix that in ME2 by reprogramming them again through Legion to create peace.
The ending also clearly diverges off into a different writing style from the rest of the series as a whole. When the rumors started going around that Casey Hudson and Mac Walters took the ending entirely into their own hands, locked out the rest of the writers, I really wasn't surprised. I really suspect it to be true.