[Note: Minor Spoilers regarding Mass Effect 3's ending within.]
William Goldman once wrote that the secret to a great ending is to give the audience, "Exactly what they want, but not in the way they expect." Bioware certainly gave us what we didn't expect, but not at all what we wanted.
The close of a franchise should have closure. Does anyone really think that Return of the Jedi would have been a better end to the series if it left us with lots of questions and no clear answers? No, and that's a static movie - not an interactive masterpiece like Mass Effect.
Without showing us the consequences of our decisions, we can't see why our decisions mattered. Without giving us a chance to have an overwhelmingly negative ending, a bittersweet ending and a total-victory ending... You cheapen the endings you do provide.
A tragedy is often tragic because things didn't HAVE to happen the way they did. The possibility, however difficult, for an absolute triumph or absolute failure is what makes the resultant ending more meaningful.
Bioware understood this even in Mass Effect 2 - making it possible for absolutely everyone to die in the suicide mission along with your crew... And Shepard himself. They also made possible a complete triumph and the survival of everyone involved.
This made the bittersweet endings most players achieved far more meaningful, and made many of us work like hell to redeem our mistakes and achieve the perfect ending on the second, third or fourth playthrough. By making the ending inevitable, you savage the power of the story for absolutely no reason.
If the ending is in fact meant to be as it is - consider this. It is being so negatively received that Indoctrination Theory has sprung up - which can be summarized as a legion of players exclaiming, "The ending is so, so, so bad, so unsatisfying, so flawed that the only explanation can be that the game's very villains are attempting to ruin the ending for us!"
That should give anyone pause. Even Starwars episodes 1, 2 and 3 didn't have audience members exclaiming that Palpatine must be mind-controlling everyone to make the characters take idiotic, nonsensical actions. So please, do something.
Run with Indoctrination Theory if you have to, or else make a full apology to your fans - explaining that you expected the ending to work better than it did and your reasons for doing this. This is my favorite franchise in existence. I'd hate to have so much of the journey cheapened by the final few minutes.