My girlfriend thru hiked the AT in 2012. Her trail name is Purple Rain. She started out with convertible pants from Rei. Those lasted about 100 miles. Soon moved to a running shorts/ icebreaker legging combo. Finished the hike out in a similar combo to this. She was frustrated by the combo for many reasons.
She spent the winter after her hike designing a hiking skirt which we took on the PCT last summer, hiking the Oregon section. The skirt uses a yoga style waistband so there are no buttons or other awkward fasteners that apply pressure with a backpack's waist belt. The skirts have pockets which allow for easy access to phone and map/guidebook pages. Easy to layer with leggings (I.e. You don't have to take off your shorts to remove leggings when getting hot. Airflow is huge she says. Also, she can stop, squat, and pee with little effort. She just started selling them on etsy and locally here in portland. Here's a link to her site for all you awesome female thrus: http://etsy.com/shop/purplerainskirts