#1) The incongruity between Padme's death and Leia remembering her in ROTJ.
#2) Anakin saying "What have I done?" after allowing Mace to get killed. This weakens his transformation to Vader a hundred-fold.
#3) Padme being medically fine but losing the will to live. No offense, but this line was clearly written by a man who has no biological children of his own. Those children would have given her a will to live. Cutting this line would have made it true that Anakin killed Padme.
#4) Palpatine's cheesy "Yes!" during the fight with Tyrannus.
#5) The voices of the battle droids and the Nemoidian in on Greivous' ship. Could they have been any less frightening?
#6) Lack of Qui-Gon. Dagobah really isn't necessary when you get right down to it.
There are other things I'd change too, but these really did detract from an otherwise awesome film (in my humble opinion).