I don't like the fact that 3.5 went overboard in nerfing some spells (they didn't just weaken them, they practically looted them): specifically, buff spells could have dropped to 10 minutes per level instead of 1 minute per level and Hold Person was totally nerfed.
I like what most everyone else likes about 3.5 core (especially DR). It is, quite frankly, better than 3E.
I dislike the bigger, better, badder syndrome of the Companion books, course, 3E has that as well in it's add on books.