I would stack Navy and Army FP programs up against any of our civilian counterparts. Can't speak for AF because I really have not worked with any of their programs.
Although I have no personal experience with FP, I bet this is totally accurate. FPs place a very high premium on training without competition from other specialists and the military seems to make this happen at many of its FP training sites.
In general, residencies which are dependent on a large volume of high-acuity inpatients and/or older (Medicare eligible) patients for training are of rapidly declining quality throughout the military. Procedural subspecialties are the most vulnerable since the shrinking med centers no longer generate the necessary high case volume, and administration boots the older, sicker folks out of the system. Gen Surg. and its subspecialties (vascular, CT, colo-rectal, surg-onc, transplant) are particularly hard hit, and the limitations of military EM training have been discussed on other threads. My impression is that some of the other surgical disciplines (urology, ortho, ENT) are declining but still treading water due to a decent volume of outpatient surgery on younger active-duty folks.
In some cases military programs may have a very different case mix than civilian programs. For instance, the ortho program at WRAMC probably has the worlds greatest exposure to complex extremity blast trauma, but very low volume of joint replacement. This is great if you are planning on spending your career at WRAMC or NNMC, but not so nice if you intend to eventually do private practice, where you will never, ever see an IED injury.
Least affected would be specialties that are largely clinic basedFP, peds, derm, etc. They also see a fair number of younger patients which are Tricare Prime, and thus stay in the military system. Training here is probably hurt less by the current downsizing/outsourcing mania, although there might still be issues with staff deployment, lack of staff retention, lack of research programs, etc.