One thing I'll never get is the whole "some characters are better than others, deal with it, the game doesn't need to be changed" attitude. This game IS already very well balanced, but by making small changes here and there, NRS can try to ensure that it becomes better still. Just because it's great, doesn't mean you can't make it phenomenal. Such an SRK SF attitude... Ugh. Anyway, on to my thoughts:
Main(s): Sektor, Smoke
Buff: Stryker and Sheeva in particular. Stryker's game is based on zoning, but with all the armor moves and teleports in this game, zoning is really minimized. Plus, characters like Kabal are arguably more effective at it, AND have better options up close. If they plan to keep him a heavy-zoning character, he could use a low projectile, whether it's a low gun or some kind of grenade that he can roll on the ground. Or, if he just becomes an overall more well-rounded character, he could use safer options up close. I wouldn't mind a buff to his roll move. It could use a slightly taller hitbox, and maybe beat out some ground-based moves. It's so easy to get hit out of, it's ridiculous. If I'm being picky, I'd like the gun to keep airborne opponents in the air just SLIGHTLY longer to allow for a little more creativity and damage in combos. Also, his grenades have WAY too much recovery to be useful (outside of hitting a full-screen croucher, as long as that character can't teleport out). The baton sweep is also totally useless. Depending on what else would change with Stryker, I would enjoy seeing the grenades get a faster recovery and slightly higher damage. He wouldn't need all of these changes, those are just some of my thoughts on things they could or should change.
I'm not sure what to do with Sheeva as I don't have as much experience with her as I do Stryker, but she feels as if she needs more help than he does. She does good damage, but that's about it.
Nerf: Kung Lao and Kabal. Kung Lao just has way too many options. While I'd personally like to see the low hat go altogether, I'd be fine with some more recovery frames. His standard hat can already be aimed low. When you compare his specials to some of the weaker characters, it's pretty glaring how much better his are. Spin, dive kick, and low hat are arguably among the best specials in the game. The only thing I'd like to see changed with Kabal is the dash cancel. I think he should either not be able to cancel it at all, or give it some recovery frames. No one else in the game has an advancing special that is fast and gives a full combo on hit that also can be cancelled and made safe.
There's other minor things I would change if I were in control, but those are the main issues I would change. Just my $.02!