well sub-zero was my favorite from mk1 - mk trilogy. then mk4 was released and quan chi was instantly my new favorite and has been since mk4. i dont even near as much like sub-zero as i did way back in the day.
Sub-Zero with Kabal hooked closely behind. Sub-Zero was the first character I ever played as on super nintendo and the first fatality I ever preformed.
When I got MK Trilogy I was fascinated by Kabal and how strange he looked. lol, I was way too young to follow the story.
My #1 favorite is Liu Kang. Part of that reason is that he is inspired by Bruce lee. Lee is my idol. but the main reason is that this man is someone to look up too. I mean this is a man who dedicated his life to protect the lives of others . A man who chose to to protect humanity over being with Kitana, I mean this guy practically gave up everything for humanity.
Scorpion is my favorite, has been ever since I first played MK as a kid. But honorable mentions that are pretty high on my list as well are Sektor and Kano.