I use;
Kenshi
Liu Kang
Shujinko (bad ass fucking combo's man)
Noob-Smoke

Disregarding Shujinko (Of course you're good with him! He has everyone's best friggin moves!) I'd say these would be the people I kick the most ass with, in this order...
Li Mei
Mileena
Liu Kang
Sub-Zero
I prefer Mileena, since she's been my main ass-kicker, since MK2, but I just kindof, got better with Li Mei, without intending too. I dunno how it happened. I figured it out during chess kombat, when she was my grunt, and at 25% I could beat the hell out of the 100%... warrior... guard... thing... I forget the name. The one that has two pieces and is next to the leader piece. In any event, that's when it hit me. And yeah, I was right. She's the only one I've actually been able to get a flawless on Onaga with.
I guess it makes sense, since she was my 3rd bext in DA, and my 1 and 2 aren't here anymore. Meh. *Shrugs*
PS. I also seem to be unusually lucky with Kira. I wouldn't say I'm good, since I haven't developed any concrete strategms, but I seem to be a natural ass-beater with her. So yeah, lucky is a good word.

My Mains:
Kabal
Tanya
Liu Kang
Shujinko
Secondary Characters:
Baraka
Nightwolf
Kira

My main kombatants are -
Scorpion; Baraka; Sub-Zero; Liu Kang; and Ermac.
My secondary kombatants are -
Jade; Li Mei; Ashrah; Kobra; and Noob-Smoke

Noob-Smoke
Shujinko
Liu Kang
Jade
Darrius
Raiden
Kabal
Havik

I can fight pretty decently with everyone (although ive found that ive started to like repeating specials alot *sigh* need to try to use more combos) except for kira and sindel. I dunno I just cant use them too well. Im sure one day im gonna get my butt torn up by one of the online but they just dont fit my groove.

Main: Sub-Zero
Secondaries: Jade and not sure of the 3rd.

Sub (I don't think anyone will ever replace him as my best or favorite)
Baraka - the reach of his blades is ridiculous
Ermac - powerful with good juggle combos