I'm looking to get deep into a fighting game, and since I have way more time with my Vita than anything else, I'm trying to decide between the two. I thought these would be good choices since I play MK and Tekken with the pad, as opposed to all others with a stick. I know Tekken 6 is an older game, but I've been told the skills would translate to newer Tekken games. What do you suggest? Thanks!

Absolutely mk9, sunk way more time into it, and the online is good.

Competitive, deep systems and playing against others: Tekken 6
Lots of single player content to keep you busy: MK9

In my experience, Tekken was always far more comfortable with an arcade stick, as the timing of the strings can be pretty particular and you don't want to spend any time moving a thumb around to execute stuff.  It is certainly playable on pads though.  More than that though, Tekken is too much about juggles for me, and the momentum generally moves in one direction too long for a fight to be exciting for both players start-to-finish.  It's turning into the next Killer Instinct, and the whole game is gradually turning into "Who Can Pull Off Their Ridiculous Combo First?".
 
MK, on the other hand, feels fantastic on a gamepad with directional buttons.  I personally feel that's the way it should be played.  The fighting is also pretty solid, and for as accessible as it is there is depth there to be delved into.  MK is a great gateway drug into fighters and a fine choice for substantial fighting in any case.  Especially if Vita is your platform, I recommend MK. 
 
Hope this helped!

MK9

MK9 for the sheer amount of content. You can find it on Vita for $20 new now if you look around while Tekken 6 is still expensive on the PSN store.

Mortal Kombat there is really no contest here.