I guess I have to be in the minority here and say MK3 was my favorite. It's the one I started with back when I played it religiously on my brother's Sega Genesis. After that going back to MK1 and 2 just felt...wrong. Everything felt so clunky. It's like playing Tekken and Tekken 2 after Tekken 3. (I did that also)

Also I could never beat Kintaro. I managed to beat him ONCE and then right after that stroke of luck, Kahn proceeded to annihilate me.

More recently I played some of the Klassic MK games on Xbox Live Arcade because my friend has it. Either I've gotten worse as a gamer or the version of MK3 I played back then was weaksauce. The MK3 Shao Kahn I remember was a pushover. But in the Live Arcade of MK3 I just could not beat him.

Of the modern games, I love Deception and I love Shujinko. Deception Konquest was the best.