I love all fighters (except Virtua Fighter... seriously... fuck that...) but if I had to pick, between these two, I'd say Mortal Kombat. I feel that Street Fighter is *better* from a control standpoint, and I'd even dare to say it has cooler characters (that's not to say Mortal Kombat characters are lame btw) but I normally have more fun playing Mortal Kombat due to the visuals (meaning blood and gore here) and I will also admit that most of my friends prefer Mortal Kombat, so that probably factors into that too.
That said, Mortal Kombat Deception and Aramageddon kinda sucked. The only Street Figher game I've picked up and thought sucked was EX3, and I heard that the EX series was OK EXCEPT for that installment for some reason...