I prefer lycra, and although I wear a skort when road cycling (for modestly), I wear regular pants on my MTB. I tried the skort, but like volklgirl, it would get caught on the nose of my seat. Scary sometimes when needing to make a quick hop on and off.
I've tried on the baggy shorts, and again like VG, I have had a hard time finding any that fit. This year, Novara had a pair that actually fit my waist and hips, but I couldn't see any advantage to them. The liner pulled at the outer layer in a weird way, plus I looked like I had on a pair of diapers. So if they don't make me look any better, I'll stick with lycra--don't need the extra layer in humid NE anyway.
Regarding covering up. For the first time last year, I started covering up during hikes in the sun--like above treeline--and it made a HUGE difference. I felt much better than having the sun bake me. So climbing in the woods, I'll be down to as little as possible, but carry a light shirt for above treeline ascents. Wonder if I should try it on my bike as well?