* Donald's characterization in this movie. Cowardice has never been his biggest flaw, or even a huge part of his personality. Not that he hasn't shown cowardice, but no more than any of the other characters. His major trait has always been his temper, and it only is really displayed in one scene in this movie (when Troubadour sings his YouSuck song). It's not like it couldn't work as a believable flaw (it had been working for over half a century till that point), Pete could say he's too much of a loose cannon, that he flies off the handle at any slight (except, you kno, the way Pete would say), and that Muskateers need disipline.
* Am I the only one who hated the Goofy/Clarabelle part? Ignoring the fact that until HouseOfMouse Clarabelle's love interest has always been Horace, she adds virtually nothing to the story. Almost everything she does outside the Goofy scene could have been done by either Pete or the Beagle Boys. She had no characterization outside of "I'm evil, but now I suddenly love you, so I'm not anymore."
* Daisy is possibly even worse than Clarabelle. She and Donald share virtually no genuine couple moments, just Daisy being bitchy to him (and not in the BST way). Pretty much the only roles any girl in this movie serves is to be a love interest or a plot device.