While I have problems with Emma Frost ( a bit too detached), Viper (a bit cartoonish) and Sebastian Shaw (a bit miscast), my least favourites were:
Juggernaut - needed a much bigger actor, one of those Europeans/Russians who are 7ft-plus, and the comedy lines were dreadful.
Fred Dukes - he was fine before he became Blob and looked silly
Agent Zero - pretty pointless
Angel Salvadore - it only made it more offensive to canon to have an Angel who wasn't the Angel of the original five. Wings looked good, nice opponent for Banshee, but not sure about the fiery goo she was spitting.
John Wraith at least looked exactly like some of the comic book art even though I cannot stand Will.i.am. Callisto sort of worked for me, despite lack of eye patch, enhanced speed and her name never being mentioned in the movie.