MK II had true effort behind it. The upgrade from the first game was undeniable, the characters were well done, as were the stages and the soundtrack, Shao Kahn was insane as a boss (possibly the first true BOSS in a fighting game, if you get what I mean) and the fatalities had thoughts behind them, to name a few of the pros. There were also the secret characters - how can anyone forget seeing Jade and Smoke hiding behind the Living Forest's trees and dropping by to leave hints on how to find 'em? That was awesome.
MK3 (and its updates) was nice and is the last of the classic games, but it's hard to take it seriously when compared to the previous two games, especially MK II. The "alities" contained lots of silly stuff and were all cut-and-paste jobs, unlike previous games where the animations were unique. Plus it's hard to enjoy some of the new actors... I am aware of why they had to change the ninjas and so on but John Turk just didn't feel right as Shang Tsung, for instance. At least the new characters were based on elements present on the series and not... err, vampires or anything like that. Oh, and they gave Shao Kahn the "it's official: you suck" line, that was great I must admit.
MK II is my choice, no doubt.