I have an MS in Ex. Phys with an emphasis in Cardiac Rehab. I'd like to make a few points.
1. I don't feel that I learned everything about exercise physiology that there is to know, however I do feel that I gained a pretty good base of knowledge on how the human body reacts to different exercise stresses. My school was not ranked in any type ex phys ranking index, but as stated, I got a pretty good basis.
2. The students in my program were pretty evenly split between PE/Kines majors and Bio/Pre-med majors. I don't believe that either group really outshined the other
3. My course load included: exercise physiology, mamalian physiology, exercise testing protocols, electrocardiography, stats, kinesiology, and research methods. It also included garbage like: "Advanced Seminar in Stress Reduction", and the "Sociology of North American Sport". Surprisingly, my "motor learning" class, was very informative.
4. My thesis was a joke. It was supposed to be on the heart's stroke volume response to different interval training protocols. My department ordered an upgrade to our met-cart (on which I would be doing the testing). I could not get the upgrade to work. At the end of my first year, my professor promised that he would get a rep out from the manufacturer to help me set up the upgrade so that I could measure stroke volume varialbles (in reality, he should have pointed me in the direction of an echocardiogram since the indirect method of SV measurement via gas exchange is not as accurate anyway). To make a long story short, the summer passed and I continued to come into the lab to try to figure out the upgrade. At the beginning of year 2, when I inquired of my major professor about the date that a rep from the met cart manufacturer would come out, my professor looked at me and said, "you still want to do stroke volume?" At that point, he gave me the phone # for tech support. It turns out that the piece of (shit) equipment that they sent out was defective and that they wouldn't send another one for free. At the 11th hour, I had to re-write my research proposal to study LT and VO2 max variables, get it approved, and launch my study. Pressed for time, I did a poor job researching. Later when my thesis had finally been accepted, I was asked to prepare it for publication with my professors name as the lead researcher. I refused. My thesis was a huge pile of steaming doo doo, that contained at least one major factual inaccuracy that my major professor forced me to include.
If my experience doing physiological research is in anyway typical, then yes, the field should be questioned.