You make plenty of choices during F3, some of which would probably have had a big impact on the future of the Capital Wasteland for years to come. It would have been nice to see the lasting effects of your choices in the ending cutscene, rather than just having Ron Perlman tell you whether you were Jesus or the Antichrist. Speaking of that ratshit ending, I hope Bethesda didn't take away the wrong lesson when they retconned it with Broken Steel. I can imagine some of the...younger players staring at their screens in disbelief, yelling, "WHAT THE FUCK!? IT'S OVER!? WHERE'S MY POST-GAME SANDBOX!? BETHESDA, YOU PROMISED OBLIVION WITH GUNS!" As utterly awful in every way as the original ending was, at least it was still an actual ending. I'd hate for the next game to just keep on going after the main story, as if your choices didn't have consequences, or as if nobody cares what you did or didn't do prior to concluding the main story. Fallout isn't TES, and Bethesda shouldn't be trying to fit it into the exact same formula.
If anyone hasn't noticed by now, my opinion of F3 has gone down dramatically over the past year or so, partially due to Crudblud's wise words, but also because I've played through the original two games and realized firsthand just how much Bethesda screwed up with the franchise. They handled a few elements of it well, but for the most part the game is simply brainless. And that might be fine for some franchises, but not one like Fallout.