I think basically everyone in here is talking mostly about either what they've seen, or who they've played on XBLA. If I were to make a list of the best players to use characters I've ever played, as in, given me the most challenge with that specific character than anyone I can remember, it would mainly consist of people I've played in person, in some cases, based on match vids I've seen.
1. Kabal - Bill, Crazy Dom is very good with him, plays him a lot differently.
2. Human Smoke - Moe and Thrower are the only Human Smoke's that I can say are impressive because of the air throw usage, and outside of standard combo exibiting.
3. Kung Lao - Lex
4. Kano - probably Moe or Thrower, Busta you've got some work to do!
5. Reptile - ded_. Most people say I have the best Reptile they've ever played. Ded_ you need some more US exposure!
6. Ermac - the only decent Ermac I've ever really played was Moe
7. Nightwolf - LaoShu, kaillera player, I can't beat his NW unless I use top 3. Another notable NW player is Crazy Dominican although I don't know if his is quite that level, I could probably beat his with more characters. There are a lot of Kaillera players who use NW because he is infinitely more effective in any type of lag.
8. Robo Smoke - Crazy Dominican uses invis better than most people.
9. Sindel - This guy Mook from University Pinball had one of the best Sindels I ever played, but that was years ago, again I haven't come across many Sindel users, DreemerNJ would probably be one of the only other Sindel players I have played.
10. Jax - The Prophet had developed the best Jax to counter any of my major characters, since then I've never played anyone even close except maybe Julian.
11. Sonya - Phi's Sonya is pretty damned good.
12. Kitana - Julian has a pretty badass Kitana, can beat my Human Smoke, CD's is more aggressive but as effective. Moe also has a devastating Kitana.
13. Stryker - I've never played a noteworthy Stryker, nor seen one that I can remember.
14. Scorpion - The only person I ever knew who could use Scorpion at all effectively was the Prophet. Everyone else uses Human Smoke.
15. Unmasked Sub-Zero - Julian Robinson has a really tough Sub.
16. Jade - Rob Sigley used her exclusively for a while but kinda left her to the way side for some better characters. Never really played a decent Jade or seen anything too impressive with her. I think she's one of the few characters not even Moe uses too much.
17. Liu Kang - Liu Kang is one of those character where it seems anyone who does use him, uses him exactly as the others. Liu Kang in general just gives me a hard time. My anti Liu character is Reptile.
18. Sektor - Julian's Sektor is pretty tough as well, he likes to use oddball characters.
19. Classic Sub-Zero - Dark Natas is pretty nasty and consistent with relaunch combos on top of his traps.
20. Cyrax - Supposedly Paulo Garcia has a nasty Cyrax that I would like to play.
21. Shang Tsung - VDO has the best Shang Tsung I've ever played against. Lex is also deadly with him.
22. Mileena - I really don't know anyone who uses her the only decent use I've seen of her is from Lex vs Bill's Kabal.
23. Sheeva - Moe's Sheeva can be downright ridiculous and he'll beat you with mostly the 4 hit kick combo and wakeup throws.