I've used both and really didn't prefer one over the other.
With National, you do go straight to the gargage and can pick out the car but when we were there, it was slim pickings. Also, once you got in the car, you had to wait in line at the check out booth. So there is still a line, just not as bad.
With
Budget, again go straight to the gargage and since this was my first time, I had no idea where the kiosk was. I just went to the little booth to check in, no wait and was offered an upgrade. Handed us the keys and we were off--didn't have to wait in line at a check out booth.
Both had clean and fairly new cars. So if given a choice, I would pick the cheaper of the two.
Hope this helps.