TheTick:
Thanks for the slack, squid...from a former flyboy!

)
Seriously though, one of my son's young friends just signed up for a tour as a sonar operator on a submarine. My son also seriously considered the Navy as well, in part because of the excellent reputation of Navy schooling. Even though the Air Force schools were good to me, I have met a lot of Navy personnel who were well trained and to me it is obvious that Navy schools are top notch. I think my son's friend will thoroughly enjoy both his training and his service.
bigTomHanks:
I spent all of my twenty years at Wright-Patterson AFB (five years active duty and fifteen in the Air Force Reserve), and I am well aware that much of the gee-whiz stuff of the military is researched there. However, I was not an engineer there, but an enlisted technician so my perspective is not exactly what you need.
However, I did get to know some folks who did (and still do) what you are considering. One friend of mine is a civilian aerodynamics engineer there, and he has done wind tunnel research twenty years ago that has been flying for some time now. And some of the stuff he is currently researching could be flying in the next decade.
Another friend of mine did research into advanced battle damage repair systems, one offshoot of which ended up as the miniaturized headset/database systems where a tech can wear an eyepiece and dynamically look up technical data as he is observing the aircraft damage. I don't know that this is an operating system on the flight line yet (been away from the military for over ten years), but it was gee-whiz stuff at the time.
As several writers have remarked, there will no doubt be some areas of a career that the military will not let you control. But the experience and the graduate schooling my friends acquired (especially if you get into the research areas) would be world class.