I also disliked Metroid Prime, but not because it was 3D (I actually thought being 3D was an awesome idea for a game themed around exploration). Rather, my problem was just that it was boring and had a lot of dubious design decisions. I actually just finished writing a rant about this so whenever I upload that to Google Docs I'll link it.
When it comes to Mega Man, I loved the Legends games. I've heard that X7 and X8 were also 3D and didn't quite work as well, but I haven't played them yet.