One thing we always have to remember is that when the pleated kilt was being developed, the Scots didn't sit around as much as we do these days, there was just too much work to do. Therefore wrinkling the pleats because you sit on them was not a major problem, and if they did wrinkle they weren't too concerned. Remember the common Scot wasn't worried about fashion.

Now, the pleats are there to allow freedom of movement (think of women's skirts and how tight they can be without pleats). Why the pleats are only in the back I can't say.