The frequent crashing. The only game I know of that crashed more than Fallout 3 was Knights of the Old Republic. Obsidian cleaned up most of the crashing in KOTOR 2, but they replaced it with missing content. Hopefully that's not the case with New Vegas.
Took away from the immersion in my opinion.
"Immersion" is such an overused word. I think suspension of disbelief is a better term to use. Anyway, I don't think they're going to get rid of that. I hate games that don't put "empty" on containers. It's harder to clear out an area with plenty of loot.
Also, I believe the repair system in Fallout 3 was broken. I absolutely HATE unique items, because it means I either can't repair them, or I have to comb the area for items that I can repair it with. I think they should have stayed with the Oblivion system, but maybe added onto it where you could only repair a certain item if your skill was high enough, instead of needing a completely new item to repair it. That makes little sense to me.