I think a good way to look at it, is rather from RTS view point (think of it as you are trying to implement a first person aspect into a game like tib wars or any other C&C game). Because then it would save a lot of time thinking about how you could fit this RTS mode in.
Another thought it that when you start a game in RTS mode, your team has say 5-10 minutes to discuss and plan how their base will look, and each player gets 500 credits. But credits are not generated during this "design stage" (another thought is that your team starts with an already deployed con yard). Alright, so your team has discussed how the base will be laid out. Now who will actually place where the buildings are going to be? The person who contributes the final amount of credits? A voted commander could be possible for this. But as somebody said above, each player could get a squad of 5-10 bots that they can command.
Victory condition? Destroy the enemy Construction Yard. But they would have to go through the enemy base to get there (possible laser fence post defending con yard for Nod, and firestorm wall for GDI?)
Also "Grab an MCV, some friends in an APC and build another independent outpost?" THAT IS WHAT I WOULD DO ALL DAY EVERYDAY *remembers above victory condition that I wrote* oh..umm..well...scrap that victory condition then!