Use Trailheads as staring and stoping points on Plans not just Towns
This would be nice as not all of us are thru hikers and want to go into town... I started the AT last year in Harpers Ferry and rode the Roller Coaster SOBO. I'm continuing this year and would like to be able to use the planner to figure out were to stop and start day to day and know where to end on major highways so someone can pick me up after I complete the section.

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Jerome Matthews III commented
This is what I have been doing. however, it throws everything off because it wants me to stop off the trail instead of going to then next shelter/campsite. For instance, my trip this year is approx. 5 days going from Ashby Gap Rt 50 in VA to Swift Run Gap Rt 33 in VA. and its not even distances per day. One of the configurations I had made me stop in Luray Va before heading back on the trail plus on that day it was like a 9 mile hike when I'm averaging about 16.
Which leads me to... what if you could add how many miles a day you can hike to the planner it would still be an approximation to where you stop but more accurate then city to city.
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This is a good idea. Once thing you could do as a work-around is to find the nearest town and use that as a rough approximation.