Sometimes less is more, this wasn't one of those times....
Yesterday I looked at why the multiple choice endings of Deus Ex: Human Revolution ended up falling short for a lot of people. Long story short I believe that Adam Jensen was a well established character and by dint of that fact a majority of the endings didn't seem to fit with how he would have handled the situation. Perhaps the opposite problem is true for what stood as the original ending to Fallout 3.
While you do control a majority of what happens in Deus Ex: Human Revolution: from what augmentations you get to whether or not you go on side quests to whether you're going through with no blood on your hands or enough to give the Red Cross a run for its money, there's the fact that Adam Jensen is not you. He's his own person, you're kind of just along for the ride. You can make some story based decisions, but they're through the lens of what he'd say anyways, and it doesn't really come up all that often.
With Fallout games in general, you are your character. You choose what to be good and bad at, your race, age, gender, whether you're good, evil, or just kind of there. Basically speaking the game gives you a lot of freedom and lets you hit the ground running.
That's why the ending really pissed off a lot of people.
Again, everything comes down to a decision regarding the future. Project Purity, something that could help save the Wasteland, is overloading, and you have a choice to make. You can do nothing, and have it overload, you can send Sarah Lyons in to activate it, or you can do it yourself. Activating the purifier is a deadly task due to the radiation present in the chamber. It's telling that the game only gives these three choices, and none of them actually lead to anything afterwards. It was only after Broken Steel that the game could even continue.
The entire thing reeked of poor planning for the most part, since as people pointed out at the time there were companions that were literally immune to radiation, but each of them provided some response as to why they would not complete the task for you. On top of that even being a bastard and inserting the modified virus that President Eden gave you into the project didn't really mean anything, because aside from a couple of lines in the ending narration changing you'd never see the results of what you did. Of course this was true regardless of the choice made.
I think that on one level, these original endings shared the same problem with the DE:HR ones, in that they were too vague and never went in depth to the consequences of any of the actions taken. This was something that Broken Steel directly remedied upon its release, giving further story elements and ending in a way that was satisfactory and allowed continuation of play if you so chose (granted there wasn't exactly much to do after that point, but that's another matter entirely).
I feel that the more choice is given to a player, the more different representations there should be for possible endings. I'm not asking for twenty or thirty distinct endings that are fully fleshed out or anything, but how about something more than "push the button, or don't". In games like the Final Fantasy series the one ending does work because the characters are established throughout the story, so as long as it jives with the motivations and (here's the important part) isn't totally vague about crap, then people will be alright with it. But for a game like Fallout, I think that having a more diverse set of endings and handling them better would have gone a long way towards alleviating a lot of the complaints.