I got the SS Jaguar a couple years ago as my first bass. Just bought it on a whim, because it looked, felt, and sounded good.
Didn't know anything about bass (still don't know too much).
I've got several other short scales now, and am pretty interested in a Mustang. The Fender Mustang costs more than
a Standard Fender Jazz or P bass. Something's a bit off there. AFAIK, the Squier Mustang is discontinued - most stores
list replacements.
Anyways, about the Jaguar. I still like it a lot. It's comfortable, inexpensive to buy, and sounds good.
I hear a lot of people complain about the J pickup being weak. I don't have that problem with mine.
If I anchor and pick right over the J pickup when it's soloed, it's just as loud as the P. Definitely a lot
different tone though - more sharp, biting, and nasally.
I think it sounds best with the P maxed and the J at about 80%. You can get a good variety of tones from it
with different knob settings and picking positions.
While I don't have a Mustang, I do have a few short scales that only have a single pickup. You don't get the variety
of sounds that you can get from the Jaguar with knob settings, but they still sound good, and you can get a fair amount
of variety from picking positions.
So - to answer the original question. My first uninformed choice was to get the Jaguar. I'm happy with it and glad I got it.
But - (there's always a 'but', right? - ha ha), I also would like to get some version of a Mustang. And probably will sometime
in the future. So, I guess the answer is both.
Right at this time - I'm trying to hold off for a bit to see what develops with this one:
http://www.talkbass.com/threads/fender-modern-player-short-scale-jazz-bass.1089586/
Modern Player short scale Jazz bass. It's not available here yet though.