Regarding the Kitana wakeups (sry. don't know the correct move names):
Its not 100% reliable since I have no one to test this. But it seems like you can hit her out of all her wakeup attempts. In general, these moves work, while not every move works on every wakeup:
d4, d4+ground hat, uppercut, F4 and obviously F2
Pretty Kick low and Ass Boost have a long startup, so they can be punished with a lot of moves. Pretty Kick at least with F2, F4 and a well timed uppercut, Ass boost with F4 and F2
Fan Lift, Pretty Kicks high can be punished with lowering the hitbox (d4+ground hat, uppercut).
Certain ex moves (EX Fan Lift and EX Fan Hit as well as regular Fan hit) need to be countered with at least 2 hits (d4+ground hat).
It'd be nice if someone would try it out and make a list. Unfortunately I can't, since it'd take half my life waiting for the KI to do the right wakeup move
Now that I think about it, I'm sure you can punish a lo of wakeups with the moves above.