Mine:
Stryker (he'll always be the fat cop from MK3 to me)
Sindel (gross and old, and way too powerful in story mode -_ -)
Quan Chi (shouldn't have been in the game, although I assume he'll play a bigger role in MK10)
Nightwolf (I like him, well the idea of him, but I just never use him, his alt is legit though)
Kano (He's needed for the story, but never use him or even know any of his moves)
+
Liu Kang (Never liked him, never will. And in storymode was seriously lame, hope he dies again in this universe)
Younger Sub will probably give way to Cyber Sub, with the hope of getting back his human form. Although they tangled that hope for use human Smoke fans for over 10 years, most MK players only knew robo-Smoke until MK9.
Reptile, although I would never want to see him taken out, kind of sucks in this game, his walk is awkward, he should be more swift like a snake or something not slow like a komodo dragon.
As for Sheeva. Hated her in MK3, but I kind of like her in MK9, especially when I use her against my one friend who likes to sit at the edge of the stage and block everything. They just need to give her a better voice, not a chick trying to sound like a guy, make her sexier.