I haven't played Mass Effect 3 yet but I get the impression the main complaint is no matter what you do the ending remains the same for the most part. That's an issue when a company advertises a game as being all about the choices. The complaints wouldn't be there if they'd called the series Minor Effect. People who have bought into the series are within their rights to expect their choices to impact the ending. There excuse for not having your choices in mass effect 1 effect Mass Effect 2 much were that it would make Mass Effect 3 too complex. Fair enough but there was nothing to stop them going off on 50 tangents in the final game other than laziness.
Everyone goes on about the ending of the game but forgets to look at the seperate endings that happen within it. You do determine what happens to many of the species and characters during the cause of the game and each mission is like a seperate ending you created. Many peoples stories are different even if the final chapter isn't. Its not the destination but the journey that matters with this one.