UMK3 gets lumped in with MK3 for me. Yes they're different, but it's like all the different versions of Street Fighter 2 for me. They were all pretty good, and they all spawned off the same original game.

Sub-Zero's no mask thing was part of the story line. The sad cyber ninja story line I mentioned. You don't have to like it, but at least they had a decent storyline reason. (for a fighting game)