I love all the MKs, which is why i have them all as im sure many of us here do. So, its hard for me to say which is my fav, but i guess they'd be in this order, no. 1 being the most liked...
If I had to pick one it would be MKII. I just loved it and still do. I am so glad it came out for the XBOX, but I wish Boon would have just released MKII and MK3 together on one special edition disc. I don't care for all the other arcade games on it MT2.
1. Ultimate MK3 (I'm such a fan-boy for this one I have one of the arcade machines )
2. Mortal Kombat Deception
3. Mortal Kombat
4. Mortal Kombat II
5. Mortal Kombat Deadly Alliance
6. Mortal Kombat 4
I really don't consider "MK Trilogy" to be one of the series much like "MK Gold" it was just a special version for the home systems, not really a whole new edition of the game.
I would absolutely die if they ever decided to make an "MK Klassic" where you would have a 2D platform with all the characters new and old (similar to trilogy) and online play.
I don't think they realize that the older versions of the game have SO MUCH staying power that just the addition of a nice feature like online play would be enough to produce great sales... I mean just look at the street fighter series, or any of the SNK fighters... I'm not saying I want A million versions of the same game, just a classic 2d fighter with online play (and lets face it, if you're not a Street Fighter fan than you're pretty much left out in the cold in that department)