Fallout 3 is still the best.
Even after all the patches that came out, they've changed very little. They fix some quest issues (the most glaring ones), but not all. But the broken quests I can understand - it's hard to account for ALL possible combinations of interactions and dependencies between various quests. The biggest problem of this game is in the technical department. It uses the same engine as Fallout 3, and comes out 2 years after it, yet it comes out with all the same problems Fallout 3 was suffering from BEFORE all the patches, plus a million of its own ones. It's like in all the years since Fallout 3 nothing had been fixed. It's absolutely inexcusable that Obsidian released the game as it did - it's like they haven't done ANY work on the technical side. None whatsoever.
Which is a shame: it could have been an awesome game.
UPDATE: After many patches the game became more or less playable. Even graphically it became almost as good as the Xbox 360 version. The performance still suffers, once your save game becomes rather large (I think about 6 megabytes of more). And HUGE slowdowns, when you travel between areas with followers - for some reason having a follower makes the game virtually unplayable due to severe performance issues,