Okay so here is basically how it plays out.
Street Fighter has a shit ton of fantastic games featuring its characters. (SSF2T, SFA2, SFA3, SF3:3s, MvC2, CvS2, XvSF, MvC and more)
Mortal Kombat has 1 amazing one (UMK3), 1 solid one (MKII) and a 3rd (Shaolin Monks) that is pretty fun but essentially irrelevent to this argument.
Now, to essentially compare the quality of Ultimate 3 to the best of the best Street Fighter games (for argument's sake, we'll say MvC2 and SF3:3s), it is a hands down, no questions asked win for Capcom. Their games are just straight up better.
Now, this doesn't mean that I don't enjoy the MK series (many here will vouch for the fact that I'm a big fan and can beat you in whatever one you want), but simply that, as a competitive level fighting game player, I can see the quality that the quinessential Capcom fighters possess that just isn't present in any games in the MK series.
As much as I love me some UMK3, the Street Fighter series is just exponentially better.
As for the people arguing about 3D, who really cares? They all basically suck for both series, with the exception of Street Fighter EX+A. MK: Deadly Alliance is mediocre at best.
For the person who argued that MK has more content (ex. Chess and Kart), let me ask you this. Why the hell are you playing Mortal Kombat for any of that stuff? It's been done better (Battle Chess, Mario Kart) many more times then I can count.
To the person who said something about Street Fighter snobs, what does that make you? I'm pretty sure that makes you a Mortal Kombat fanboy, which is basically just as bad. Besides, we're not snobs, we're just correct

.
To anyone else who thinks Mortal Kombat, before you bother to type out your oh so compelling argument, sit down and play Ultimate Mortal Kombat 3, Marvel vs. Capcom 2 and Street Fighter 3: 3rd Strike all in a row. You'll see what I'm talking about after a few minutes.