Shiki is definitely wearing a mini skirt and that's sort of the point. The game was all about the biggest fashion district and mini skirts seem to be doing well as a fashion item. Rikku (X-2) also has a bulltrout short skirt but that was fan service.

I didn't look at many of Yuna's outfits in X-2 but her default is actually just hot pants so w/e there. Tifa's skirt is short but it's still longer than the others.

At the end of the day I think it is important to realise two things. 1) sex sells. 2) these characters have disproportionate bodies; their legs are much longer than their torsos, which gives the appearance of a shorter skirt. Not to say they aren't short, but it just makes it look worse.