To me it makes more sense to train, at during long runs on the road in pants the same way it makes more sense to wear sneakers than flats. The knee and ankle joints will be the most mobile if warm so it reduces injury, and the small amount of resistance the pants add is good for strength.
I mean people are going to think I'm trolling with that last part but, running in the rain is good for strength because the wet clothing adds weight. Running into the wind in pants rather than shorts takes a tad more strength. Same as does maintain a given speed in sneakers vs flats.