The "no show" is a serious problem. A few years ago I started a trip at New Found gap. When I got to Gatlinburg, I stopped at the backcountry office for my permits and they were barely able to squeezed me into a couple of shelters. Sorry, Icewater springs is full, there is one spot left at Pecks and two at Cosby knob. But when I get to these places they were almost empty. The weather had turned rainy.
Even with the new fees, I doubt it will help with the no show problem. That's the thing which most concerns me. It's not apparent that a thru-hiker can get a permit if the system thinks the shelters are full.
Anyway, I can understand why they want a system like this. For one, it makes it self serve for the most part so they don't have to deal with the permit thing. Second, they are trying to manage a limited resource (space in shelter) which has high demand. You really don't want to show up at a shelter site and have 80 other people there do you? That could happen if it was a free for all.
All in all, it is a pain and just one more issue to deal with which we'd rather not. This is more then just passing interest to me, I plan on hiking through there again this spring and will have to deal with it one way or another. Last time I just put a blank permit on my pack. I was hoping someone would ask to see it, but no one did.