The Fender short scale set sounds quite good, but personally I don't care for the small gauges and soft tension.
I've used DR short-scale sets, both Sunbeams and Hi Beams, and they sound great. The Hi Beams in particular sound really rich on the Mustang, especially with the tone rolled off a bit. But again, I don't find these have enough tension for me, though they are definitely beefier than the Fender short-scale set.
The biggest problem I've found is that many E strings seem to get a bit floppy and give a soft, pillowy sound on a short-scale bass. I spoke to the folks at Birdsong about this (as I'm planning to get one of their short-scale basses one day), and they said they've found that higher tension strings will tighten up the sound.
So, last night I put on a medium-scale set of D'addario 50-105 nickels (EXL160M). This is the biggest, highest-tension set I can find that will fit the Mustang properly without cutting down a long scale set.
I really like them! The E string definitely sounds better to me. If the tension ratings at D'addario's web site are accurate, the medium-scale .105 E string has over 20% more tension than the .100 (34 lbs vs. 28.) I would think the round-core E string in the DR sets, while measuring .105, are probably closer to the D'ad .100s in tension.
To my ears it makes a difference. Your mileage may vary.
I did have to make a truss rod adjustment going from the DRs to the D'ads; I did a half-turn and the relief was still a tad high this morning, so I may need to do another quarter turn. What a pain! Why couldn't Fender make the truss rod more easily accessible?