I'm a board certified medical practice executive. I run medical practices for a living, also consulting with medical practice clients to help them run more efficiently. I feel your pain.
In all of these instances, the problem is probably not the physician--it's the person running the office. There are a number of reasons that wait times extend well past the appointment time. Almost 90% of those can be fixed if the office just works out its inefficiencies and changes how it runs. Medicine operates in the 21st century, unfortunately, most offices still run like it's 1955.
On the other hand, many physicians also think that they know enough about business to run their own office. Those are the ones I'd like to take out back and beat with a stick, because their offices are typically in the worst shape. And it's their patients who suffer the most.
The bad news (as Tim #3 points out): the new insurance "reform" legislation is only going to make this worse in a few years, compounded by the lack of primary care doctors in many markets.
The good news is: I should be gainfully employed for some time to come.