For pants- pockets and lots of em. Also, something great would be snaps or buttons on the inside of the pants, so you can make a cuff, then double it over and button or snap it down so your pant legs don't fall down all day. I walk around with my legs rolled up cause it's easy and it's a sign that you ride to others in the know.

Ventilation with biking in mind is a great idea. Keeping your crotch cool with some kick as ventilation would rock. Oh, and no chamois, or at least make some without a chamois.