Hello everyone...this post is the result of a week of steady work. Maybe others figured all this out long ago, but I've just arrived at this point.
Here is my Aesthetica model (MH Alpha 5.1), with a pair of jammer shorts. She starts with a jumping jack, and then walks away.
The goal was to create a pair of pants that could successfully move through athletics, with the minimum of planar intersections and distortions.
The solution here was to start in the middle of the groin, and using both retopology and proportional editing, create a mesh that both moved and folded naturally.
Note that there are no shape keys in the final pair of pants, and only a single level of subsurface subdivisions.
This leaves me free to create whatever types of folds I wish to add to the realism of the model and its movements.
A jumping jack, from the front:
A jumping jack, from the rear:
Blender heads can try the model themselves:
http://www.geekopolis.ca/blender/walk_cycle_models/jammerShortsBustier1_263a.blend