3.

To break it down faster:

Gameplay:MK3 easily

Storyline:Me personally I like both, but some will go with MK2 over MK3 and vice versa

Characters: MK2 added the best new characters IMO

Darkness:well all MK's are dark but MK2 had this creepier, darker feel to me anyway

Fatalities:MK2 by farrr

Secret characters:MK2

Both games are great though IMO, but I like MK3 more

MK3 man!it has better gameplay and u can beat ur opponents faster with ur combos and attacks