I think the best thing you can do is not put to too much emphasis on running on time. Doctors never run on time. If the wait is this long, consistently, find someplace else to go if you have a choice. Usually they try to run on schedule, but I have found that between waiting room time and then the "teaser wait," when they put you in a room, you're easily behind schedule by 15-20 minutes. I have had to wait longer and have also been seen very quickly. I have expressed that my time is valuable too, and we know they know this and surely they do their best to remain on schedule. I have asked the receptionist if this long a wait is typical. I can certainly find another doctor if this is how they generally run their practice.
Not too long ago, I was in the waiting room for more than an hour. They asked me to be there a half an hour early for the paperwork process (quite a bit of it). Then I waited another 45 minutes to be seen. I did ask the receptionist if this type of running behind schedule was typical, to which she replied that no, it was not, and this has held true. Again, I expect a delay, but I have no intentions of having to sit 45 minutes past my appointment time with any regularity.