I almost always wear shorts on my flights also as it's normally not cool enough for me either. However, I usually layer my upper body with a dri-fit t-shirt, shirt/sweater, and have a jacket handy. If I do get chilly, I just toss the jacket or blanket over my legs and I'm fine.

On the other hand, my buddy never wears shorts for fear of needing to jump on the emergency slide and skinning the heck out of his legs .