My biggest issue with the ending of Fallout 3 was that it fell into the trap of "sacrifice in place of theme." A lot of video games end with the protagonist making a heroic sacrifice and I automatically deduct a large amount of good will from the game as a result. I consider it one of the most singularly lazy storytelling tools and think it's written by people who generally don't have any actual skill in writing. About the only exceptions I make for this are Infamous 2, Dragon Age: Origins (if you choose to die), and (of course) Planescape: Torment.
In the case of Fallout, I felt the game's idea of sacrifice was bullshit from the beginning and the game didn't help the matter because your father died for a very questionable reason (only temporarilly delaying the Enclave in activating the Water Purifier--which isn't a bad thing since the WP ISN'T a superweapon--yet) and because you die when you have a Super Mutant beside you who can take the risk yourself.
I agree the original ending was crap, but at least it gave you some kind of choice, and at least it stuck by that choice.
Broken Steel took the only choice which had any impact on the original ending and decided it was meaningless. Because the same thing happens either way, there is literally no consequence of deciding to sacrifice yourself(Apart from Sarah Lyons staying alive). The only meaningful choice in the game is no longer a meaningful choice.
Plus, there's the issue that selling a new ending to the game can mean one of 3 things:
A. Bethesda didn't realise that the ending would cause controversy in the first place (In which case they seriously lack critical thinking)
B. That at the time they genuinely did think the finality of the ending was the best for the story despite what people say, but then when push came to shove decided to go back on it(In which case they care more about either profit/crowd pleasing then they do about artistic integrity)
or
C. They knew very well people would be outraged by it, and had planned this from the beginning, intending to cash out on the outrage by selling a £10 DLC fixing the problem they knew was there (In which case that's bad business practice)
See the problem here?, There is no way that Bethesda can justify selling an extra ending to the game, without it reflecting badly on them as a company.
It's the Inconsistent Triad of Bethesda Games.