Seems that the RTS/FPS crossover would be more fun for the FPS players than the RTS ones. I wouldn't know, I've never bothered to play one myself, but I think I'd have a lot more fun picking up orders and doing missions from an actual human player that I can talk to to give me supplies to help me on my mission than sitting back and hoping that the guy I picked to do the job isn't a total dick and won't just take your money and run. Still, kinda adds some realism since the world is like that. People are dicks, there's no escaping that fact, and FPS players are probably the biggest dicks of them all; I should know, I am one.
It also brings into question of who has the real power here. I mean obviously the commander has command of all of his units and a base the size of Texas, but once a merc is involved then it's really the merc who calls the shots because they can just tell the commander to go screw themselves and sabotage the mission if the commander tries to push things too far. However, the commander is the one who has the cash and the stuff that the merc needs so there's a little bending to the commander's will to do if you want that shiny new gun, jet fighter, APC or tank.
It's kind of symbiotic and would work in theory, you've just got to know who to trust; which, as I said before, when it comes to FPS players that's no easy task.