In terms of the entire series, I'll maintain MK2 was the pinnacle of the early years. Hated the addition of the run button, but MK3/UMK3 was still very good. MK1 I don't even really rank among the others. It still can be fun but it just seems like more of a novelty than a game to me. Weird to think about what would have happened if the original idea for it to be a game starring Van Damme actually happened...for all we know it could have killed the series before it got going. Well, either that or Van Damme would have found a second career as the face of Mortal Kombat.
MK4 is my low point of the franchise (discounting non-main series crap like MK Special Forces, that is). I know they wanted to move forward but I really wish MK4 had been another 2D game.
Once they got to Deadly Alliance I know a lot of people jumped off, but I didn't mind it at all. I'm not a hardcore fighting game fan, I didn't care about the "dial a combo" debate or how shitty people seemed to think the engine was. I had fun with it, my friends had fun with it, and as usual the storyline/atmosphere was light years beyond any other fighting series. Deception was another step in the right direction, not so much with the fighting engine itself but all the extra stuff, and the storyline in that one was even better. Loved the Konquest mode expanding on the mythology. Armageddon was just sort of an MK Trilogy redux to me - not to say I didn't like it, but it was another "CRAM EVERYONE EVER INTO THE GAME!!!" release.
MK vs DC I liked ok, but after the massive roster and metric ton of stuff that was packed into the last few releases, it was too bare-bones to hold my interest for a long time.
I'd honestly put this new one at least tied with MK2 for the top spot. There is a good balance of sizeable roster, extra features, and the fighting system is significantly more fun than the last several games.