While I can appreciate the non-stop virtue of the AT ... I think a "limited-stop" would not take away the quickness of the train as compared to normal scheduled trains.
As it is now, someone from the Jacksonville area must drive well over 2 hours south to board a train that is going to take them back north to the station in Jacksonville. (It is my understanding the train stops in Jax to receive fuel, water and minimal servicing) In reality, the drive to the depot in Sanford from Jax can take quite a while since traffic can be problematic.
It seems to me that a car loading facility could be established in Jacksonville, especially since the area by the station already receives cars by rail, allowing people in the north part of the state to load in Jax instead of having to drive south just to go north - the pre-loaded car could be appended to the train coming from Sanford or removed for the train coming from Lorton.
This would make using the AT much more attractive to those in the panhandle area.
But then, I think there should be auto-trains heading to other destinations ... like Chicago and the West Coast.