as one who has will receive his AEGD certificate tomorrow morning when i finish checking out of my command, the difference is one of focus.
my program was a broad range of general dentistry. a little (or really, a lot) of everything. ortho, endo, perio, TMD, oral surgery, prosth (rem & fixed), oral medicine, implants, lit review, didactic, CE, little on call time.
my GPR buddies over at portsmouth have had a very different year. they are essentially OSBs (oral surgery bitches). tons of 24 hour call, prep work of OS surgeries, post-ops, much less rotation time in general dentistry, more rotation time in medicine/surgery/anesthesia, etc. they are like oral surgery pre-residents. which is great is you want to be an oral surgery (3 out of 4 of them do).
i made the best choice for me, but hopefully this gives you a little insight into a couple of Navy programs.
also, these two year 'AEGD' programs arent really set-up for new dental graduates (though a few have gone to the Navy one up at Bethesda). the comprehensive dentistry program is more for career guys who arent going to specialize in one of the ADA recognized specialties, but who desire extra training, specialty pay in the armed forces, as well as promotion opportunities. 'comp trained' dentists are specialists in the military's eyes, though if they went to private practice and called themselves "comprehensive specialists", no one would know what they are advertising. as a new dentist, the one year AEGD/GPR is really sufficient to get your feet underneath you and out into the world.