The "problem" with the ending is that it allows players to quickly and easily see behind the curtain. One can easily reload the game, finish the final portion, and see the other endings without much trouble.
What people don't seem to put together is that, by and large, NONE of your choices matter - it's a pretty convincing illusion, but the vast majority of the game is the same regardless of what you choose to do. Sure, a few characters live or die, and the objectives are assigned by different people, but overall the experience is nearly identical. The CHOICES you make are what matter to you, and since most people don't play through a second time, they don't see that the results are only superficially different.
In order to have a coherent, logical ending to the game, the choices were whittled down. I can't imagine the ending the fans seem to have craved, wherein every tiny choice is given an epilogue. Did you really want to find out that saving the Rachni was the wrong answer, or curing the Genophage doomed the galaxy - and there's nothing you can do about it now? That choices whose results you can't POSSIBLY have foreseen were "wrong?" I don't see that as an improvement.
Granted, there are some plot holes in the very end - probably to be filled in by DLC - but these are no more or less severe than what we see in the theaters every summer.
To create a cohesive, narrative vision, your choices throughout all three games only matter superficially - it is a testament to the talent of the team that many people didn't notice until the ending.
