You can't go really low with short scale. Thats why all of them are usually standard E A D G tuning. I have yet to play a short scale bass with the same definition as a longer instrument.
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Only a couple relatively minor disadvantages:
1) I find that tuning a short scale bass with standard tuner gear ratios requires patience.
2) Sustain may be less compared to a long scale.
I haven't experienced either of these problems. How in the world would tuning a string that is 34 or 33 or 32 different. I also have a 28 and still no difference.This is what I have found too. I swapped out the machine heads on my Jag short scale to try and get better tuning and to minimise the neck dive. It helped both but only a little. Tuning is still more touchy than my 34" Godin. Putting on the half round strings helped up the tension a bit and now after playing flats on my Godin I'll be putting some flats on the Jag to get a bit more tension.
The Godin certainly has more sustain than the Jag. Some of this is undoubtedly due to the higher tension however some of it could also be the bass itself.
As someone said when I was researching my first bass purchases, the short scales appear to have a bit more "thump" while the long scale has more overtones and piano type sound to them. Each to his/her own tastes. I tend to play the long scale more these days but that is mainly due to it being a much better bass overall than anything to do with the scale.