No question that the romance aspect was botched. Padme is a strong, likable character, but she is lessened by falling in love with Anakin for seemingly no reason. If only we had some kind of reason. Something?!?
Seeing Yoda fight Dooku was painful for me, and it ruined any suspense we might have had about Yoda's big fight with Sidious in Ep III.
Inconsistencies (more to do with Ep III, but they still spoil my enjoyment of Ep II):
1) Anakin starts down the dark path in Ep II, only to again be Mr. squeaky clean at the beginning of Ep III. WTF?
2) Palpatine is starting to age and show signs of the Dark Side's influence. However, he is miraculously rejuvenated again in Ep III. Super WTF?