Exams are getting breifer and less detailed as time goes on, so don’t set your expectations too high.
Because exams are generally briefer and seem less thorough, you need to do whatever you can to utilize the time with your doctor wisely.
A few suggestions...
Most importantly is to have a full list of your current meds, conditions, and current issues and concerns. That's important. If they have an online registration system (most now do, especially a large hospital), I'd fill out all of that information ahead of time before you arrive for the appointment. That way you're minimizing the chance that they'll take time away from your actual exam just to do the paperwork.
In addition to filling out their forms, I also like to keep with me a short post-it node with a recap of my meds and my current concerns/issues. That way when I'm sitting there talking with the doctor (dressed or not), I won't forget to tell them about a particular issue that's concerning to me.
Does this hospital/doctor offer consulting "get acquainted" visits? If so, maybe you could schedule one of those ahead of your actual physical (although it's probably too late to change that now). That way you could go and meet the doctor for 5 or 10 minutes without any expectation of an actual hands-on exam. That's an opportunity to go over your history and concerns without taking away time from the actual hands-on exam. It also gives you an opportunity to see if you like the doctor and whether you think they'll be thorough. That way if you don't like them, you don't blow your once-a-year-physical on this doctor. You can still make another appointment with someone else (hopefully).
Also, I'd call the scheduling department/front desk and verify how they have your visit scheduled. Is it just a new patient office visit? Is it a wellness check? Is it a comprehensive physical exam? What terminology do they use to describe your scheduled visit? Also ask how much time they have allocated for your visit? If they say it's just a new patient visit and they have 10 minutes scheduled -- then there is something wrong. Reschedule and make sure they know that you want a comprehensive physical examination.
Good luck and let us know how it goes.