The only Fallout game I've played is tactics and that one wasn't so good. Actually, I found the first few missions decent, but as my characters got stronger, the gameplay just become more and more dull.
One improvement would be to let an actual writer write the dialogs and create the plot. Again, I haven't played Fallout 3, but I've seen enough of the dialogs to realize whoever wrote it wasn't competent at that job. I don't think this will be a problem with Obsidian though.
Fallout 3's battle system sounds more fun than the turn based ones. In theory, a turn based system will allow for more strategy than Fallout 3's FPS like system, but I'm not holding my breath over the idea that I'll get a strategical system period. In general, RPGs end up not requiring much strategy at all.
I do however want some modification. For example, I think the AP formula is AP=65+2*Agility. I would suggest a formula more in line of AP=50+5*Agility. Basically, agility will matter more. Ditto for other stats, I want it to very much matter which stats you choose to invest in.
Traits sounds nice, although my experience is that there's the ones that are great/potentially great and there's the ones which matters very little. Seriously, despite never having played the first Fallout, I can tell that Fast Metabolism does very little and it's effects are barely noticeable. If a trait doesn't have a significant impact, it doesn't need to exist.
This does however make me think of healing. I would like instant healing to disappear period. When you use a stimpack, I want it to make you regenerate hitpoints very quickly, like you heal X amount of hitpoints over ten seconds or so. I don't see the need of instant healing other than cheesing the game.