I wear both, depending on the ride and terrain. If going for longer rides, where I might be encountering thistles and heavy brush, I definitely wear a baggy shell. Also, the one time you have to stop and fix a flat on the trail you will wish for the baggy shell. All kinds or things can get caught in the lycra of a roadie short.

I no longer wear shorts where the lining/chamois is attached. Those liners just never seem to fit right and the chamois is all over the place. I cut all those out and now wearing a good cycling (roadie) short under the baggy shell. Just fits better and feels nicer.