The total amount of completed quests, and notes, has really climbed. Enough so that when the Pipboy is switched to Misc and Quests, the whole game slows down, or skips a few times. On occasion it freezes. My guess would be that there is just so many Quests/Notes between FO3 and NV and it's a lot to process.
I looked for some kind of way to remove completed quests or old notes, but my modding experience lies elsewhere.
It is a small idea, but I'm betting as more and more people start playing and completing the game, it'll happen to more people. So, if possible, start removing any quest passed the 50 mark in the Pipboy. Something like that. Maybe 100 for notes/Misc?
I have yet to encounter any major bugs/flaws with TTW. It's incredible, so I'm sure the next update will include a lot of fine tuning.