I have some Dare2B outer shorts which I love. Mainly because of a zipped pocket on the thigh top which I put my phone in.
What other short have a small pocket on the thigh top like pilots used to use for notes and navigation.
Dunno about thigh top, iRule (Ninjas) have two small pockets on the side, as do my Raidlight running tights.
Endura Humvees have two zipped main pockets, and a small zipped pocket lower down on the top of the thigh.
By a pilot type pocket - Are you wanting to see the phone there? Or just looking for shorts with a good, safe pocket for a phone?
Sombrio shorts have a clever pocket for phones that works very well (although not so well with newer, wider smart phones) The phone ends up beside your hip as you ride and doesn't get squashed, and althought theres no zip it doesn't want to fall out either. It works so well you don't even know the phone is even there which can be a little disconcerting.
Shame they can't equip their clothes with any sort of zip or fixing that functions properly though