To me, it all evens out. Yes, if you drive you won't have to wait for a bus. But you'll have to pass through the parking booths, wait for trams and walk to and from your car to the tram. At some resorts (the GF comes to mind) you'll be parking a long ways from your room. At others, you'll be able to park right outside your door.
I think it all comes down to what you prefer. If you enjoy driving and have your own car or don't mind renting one, then by all means drive. If you are like me and fly in and don't want to pay for a rental, enjoy having Disney drive you around! There will be aggravations here and there, but as long as you always allow plenty of time, it shouldn't be stressful. And of course, I enjoy the fact I can drink what I want and not have to worry about driving!
I'll add that in 13 trips we have rented a car over half the time. I used to be able to get better rates and now, I go for longer stays (last trip was 16 nights) and that adds up. Also, once ME came into play, it just seemed dumb for us to rent. We've always had great bus service overall.
I think its just a preference and will be different for all people. If I had stroller aged kids, that might make a big difference. But I must say, for the four of us with two adults and two teens, the busses are very nice and work very well.
To me the key point is that there is no quick way to get around WDW. You'll be waiting for trams, monorails or ferries even if you drive and walking to get to your car, bus or whatever no matter what you do. But overall, to me it evens out in the end anda there are a lot of variables to consider.