Well, drivers have to eat and need a break too. They aren't just sitting there to annoy people. All drivers and buses work on a shift schedule and it is tight. Every minute of the shift is accounted for, whether it be arriving and leaving a bus stop or having lunch. They might even be waiting for their actual time to kick back in after covering for another bus that got unavoidably delayed and now they are trying to get back on schedule. They can't just throw the system completely out of balance because you want to get someplace quicker. That could cause problems down the line and just make the situation worse. Remember you are on vacation they are working. I'm sure you take lunches and take breaks when you work. I don't think you want a tired/exhausted driver hauling you around in a 12 ton vehicle. I would think you might want a driver that is alert and rested. There is far more complexity in how a public transportation operates and you are only experiencing it at whatever point of time that you present yourself into the scenario.
Like I said, if it isn't something that one can tolerate then bring or rent a car and come and go exactly when you want to go. As for the buses if you chose to rely on them then you also have to anticipate the possibilities and "the way it is" factor of such transportation. They provide it but they cannot cater to each of the thousands of people that might be staying on WDW. It isn't a limousine service it is multi-person public transportation.
BTW, they didn't promise you "top notch" bus service (whatever that is) they offered you a free ride on the bus to your onsite destination. It will not always fit perfectly into you personal schedule, but it is a very expensive service that is incorporated in whatever charges you are part of. Your portion of it is very tiny. It's the rest of the place that is ungodly expensive.