I'm currently in the US Army. I work almost entirely with Air Force, went to basic at Ft. Jackson, and have seen Marine Drill Instructor training at Paris Island. I can say that a person's job is more important than his specific branch. In theory, all basic training is the same. The Marine Corps will tell you their's is the hardest, and it's sort of true, but its not like the Army is holding picnics and bake-offs with new recruits. Honestly, anyone coming right out of basic of any branch is going to be in good shape, familiar with firing a weapon, etc. These sorts of skills tend to fade a bit over time unless practiced. Thus most Marines will be better at Soldier skills than, say, a typical airman because the Corps treats everyone like infantry while the Air Force thinks it's foolish to send a finance guy to fire a bunch of weapons all the time. Even in the same branch there are differences from one guy's experience to the next; my cousin's basic training was considerably more "chilled" than mine.
For your game, assuming characters are meant to represent the kind of badass heroic types typical to RPGs, you're safe to treat all branches the same. Despite what the grunts will tell you, there are tough special forces types all over the service. They are more common in some branches, sure, but even the Air Force has its Security Forces (cops) and para rescue guys. Army has infantry, cav scouts, Rangers, Airborne, etc. There are Navy SEALS and elite Marines.
You might want to distinguish between combat troops and combat support. I, for example, am a TV and radio broadcaster. I can shoot an M16 and I'm in better shape than a lot of 32 year old gamers, but I'm no Rambo. Guys like me are probably better suited to NPCs unless your campaign centers on traveling all over the world and editing a bunch of video. I don't know your Nexus system, but in 3e D&D terms a Soldier like me might be an NPC class kind of like the aristocrat; ok at fighting and decent skill points. An infantryman would be a warrior. Special forces, PC types would be fighters and rangers.
Officers start out just like the rest of us, they aren't really "higher level" just higher authority. They spend their training learning leadership, war strategy, and other skill point type stuff. Keep in mind that a young commander, say a Lt. with a couple years in the Army, likely has an NCO with more than a decade of experience (sometimes a LOT more) working right under him. The officer outranks the Sergeant because he's an officer, and has certain specialized leadership skills, but is he several levels above the more experienced guy, with the HP and BAB that comes with it? Not usually. Like everything, though, there are exceptions. A Lt. who served as a squad leader in Vietnam is probably "tougher" than a computer network Sergeant First Class, regardless of how long the latter has served.
I'd say, make some distinction between combat and combat support. Use feats to represent special training like Airborne. Make prestige or advanced classes out of specific special forces groups like SEALS or loose archetypes like "grizzled combat veteran." Officers are just like normal guys except with a different set of skills, and they too range from desk types to special forces leadership.
Finally, a note on terminology; the Army has Soldiers, the Marine Corps has Marines, the Navy has Sailors, and the Air Force has Airmen (even the females are called Airmen). Oh, and there's a Coast Guard, too.
