Scorpion and Sub-Zero for me, mostly.
Actually I still recall my "mains" for each games I played the most (main + good alternate).
MK1 (Arcade first, then console ports after): Scorpion / Raiden (honorable mention to Sub-Zero which I played mostly on the Genesis version).
MK2: Scorpion / Johnny Cage (honorable mention to Baraka, played him quite a lot too).
UMK3: Smoke / Scorpion (honorable mentions for Cyrax and Nightwolf).
MK4: Scorpion / Jax (didn't play MK4 much though, mostly played the Dreamcast version's MK Gold; but I never really was a "fan" of MK4 in general).
MK Deadly Alliance: Scorpion / Kenshi (and a bit of Reptile play time too).
MK Deception: Scorpion / Nightwolf (and some Ermac as well).
MK Armageddon: Skipped at the time, never really got to play it. It was a period of 'Lost interest in MK' which lasted a number of years and I generally moved away from Fighting games.
MK Vs DC: Same as the above with Armageddon (but I did watch the Story mode on YouTube).
MK9 / 2011: Brought back my interest to the MK franchise and played a lot of Scorpion, Ermac and Reptile in that one. Also tried pretty much all of them really.
MKX XL: Initially (before the XL update) of course I mained Scorpion mostly, but I almost equally also played Sub-Zero (he's amazing in MKX, my favorite overall version of Sub-Zero). After the XL update (mostly played online) I played a lot of Ermac and Mileena. Comparatively to MK9 I played pretty much all the roster in MKX at least for a time (but never "mastered" any one of them).
MK11: Skipped, didn't buy. But I watched the Story mode on YouTube (along with the Aftermath expansion). After MKX I had enough of a fill with MK once more.
So for me it's really always been Scorpion, love his story, appearance, moves; just amazing character (still to this day my favorite Fighting genre character ever).
I'm still curious to see what they'll do with MK next. But to be honest at this point I'd be happy enough if they did finally decide to remaster the original trilogy of 2D MKs. I mean they could just focus on remastering MK Trilogy really, just that one and it's enough. My favorite 3D MK game is still MK9 overall (very close second is MKX). But I still - to this day - prefer the 2D MKs; especially UMK3 or MK Trilogy, either one can't go wrong.
But anyways, Happy Anniversary MK (indeed, still my favorite Fighting games franchise in general to this day).