I think the worst change in 3.5 is the new Weapon Size System, followed closely by halfing Spell Focus feats, and thirdly Wild Shape not granting all Supernatural abilities. Aside from these, the only other thing I can think of is that it takes just as much to specialize in Necromancy as it does in Transmutation, and you cant even take Divination as a prohibited school. But I can learn to live with the last one, but no such luck with the first three.