I moved both my campaigns over to 3.5 shortly after it came out, and my only regret is that I didn't do it sooner. 3.5 fixed nearly everything that I disliked about 3e, and even most of the "what were they thinking" kinds of changes I first saw (square sizing, weapon sizes) have turned out to be changes for the better.
There is only 1 thing I dislike about 3.5, and that is the Gnome favored class = bard. Otherwise, every other change has been for the better, IMHO. I also wish they'd give us web updates for some of the remaining 3e-era books such as Monsters of Faerun.