Gimme MK2.
While the whole classic game series was cheesy as hell, MK2 had the 80's ninja B-movie feel perfectly done.
Better character designs, better fatalities, some of the best stages of all the series, a really eerie soundtrack which helped to build a total mysterious ambience and creepy atmosphere.
Ninja costumes were the best also.
MK3 on the other hand (and further entries like UMK3 and Trilogy) were completely over the top and lost the mythical, mysterious, and kinda "this is a serious gore game" tone that the first two had.
They had interesting additions in the gameplay and technical department and some pretty new cool characters, but nop, I don't think they were as good as MK2.