I don't think Mass Effect 3, even with the ending, was a horrible game. But even without the ending, I felt Mass Effect 3 wasn't a particularly great game either. The only improvement from the previous game I saw was in combat, everything else, levels, story, characters, art design was at best the same as Mass Effect 2, and sometimes even worse, not to mention the fact that a lot of content that should have been in Mass Effect 3 wasn't, such as Vehicle Combat, proper Side Missions,and a climax that at least lived up to ME2's Suicide Mission.
And then after that you have all the FUBAR with the fanbase with Day-1 DLC, the ending debacle, Tali's Face, etc. and the poor handling of the harsh criticism. Granted, how the community acts doesn't actually impact the game itself, but it's a simple fact that ME3 has a tarnished reputation, regardless of anyone's viewpoint.
Bottom-Line, there had to have been a better choice for game of the year.