The thing is that you aren't in either navy. You never get ordered to do anything and you aren't obliged to take the naval rank missions (if you want to rank up, you can just wait until you find one that suits your playstyle). At best you are in something equivalent to Air America and not the USAF. Essentially you are a private contractor that sometimes works for whichever power.
This.
When I was doing the naval rank-grind, I always thought of myself as Nick Cage's character from "Lord of War".
It'd certainly be nice if there was more variety, more rewards and the possibility of bad things happening if you were found, say, shooting up Fed's in your Corvette but I don't have any real problem with the idea of being an "middle-man" character.