I prefer onsite. To me, E-Ride, Extra Magic Hour, and the busses are WELL worth it. Especially when I stay at the value resorts. I am usually so bonked from going all day long, I'm nearly sleeping on the busride back. Better than in my car. (I still get a rental car to get food, and go to universal, take trips to downtown disney) Waiting 15-20 minutes for a bus is not a big deal to me. I guess everyone has their issues.
I also agree about the all around ambiance of the place, vs. just a regular hotel. The rooms are small, but if you are going to vacation in your room, save the admission ticket price and stay at one of the more expansive properties like AKL. I say, stay on site. Pro's far out weight the cons.