Yeah - I think this time playing it, I have to accept all the bits of Mario 64 that haven't aged very well at all. The worlds are interesting but it really could do with a spruce-up.
Having said that, as well as the things already covered here, my sister's been reminding me of horror stories in Mario Sunshine. I really don't get all the people that insisted that it needed a remake as "the best one" - there are some really un-Nintendo-like design choices in there. Are you having fun getting 100 coins? Which chapter did you jump in at? The wrong one, eh?