I've done almost exactly what you're describing. My buddy and I have had an on-going sci-fi campaign for over ten years and it's gone through multiple 'focal points', from starship operations, to groundside ops of various sizes, to running a small multi-star government.
The core combat system we've always used has been the Ground Zero Games trio (Full Thrust, Dirtside, Stargrunt), partly because we like the games, and partly because the authors designed them with a degree of compatability (the FT supplement More Thrust adds on rules for cargo demands for carrying ground forces, for example).
While that system worked for us, I think with some thought pretty well any combination of tactical rules could be made compatible. I think the key thing is consistency, so that the players know how much ship tonnage they will have to get together to deliver a groundside combat group of a given size to its target. Relying on handwavium is probably not the best idea, IMO.
The other key thing in my campaign has always been economics, as that is the underlying limit on all military operations. At first we were pretty loose with it and I found the player got a bit 'out of hand' with being able to upgrade his forces between battles. He was particularly prone to using veteran troops with big kit, always. So we instituted a much tighter set of logistical requirements, and lo and behold, he had to start making some careful trade offs, like deciding when to commit his heavies, and when to use 'the rest', because if he used his heavies all the time he would exhaust them… Same thing with the naval part – we quickly found that economic constraints brought a degree of balance into games and made scenarios more interesting. (In one-off games escort and cruiser ships were not much use, but after trying to use capital ships for routine customs patrols, and nearly going bankrupt, the player found that the lightweights were actually pretty useful!)
I've used several economic campaign systems and I think most can be made to work. I like Victory by any Means, and use the Starfire campaign rules for my own stuff. I would say, pick one with the smallest amount of book-keeping you can manage, for the amount of detail you want to game.
Also, characterization is very important. The main reason my campaign has lasted so long is that the player has invested himself in his units, the characters of the leaders, and has a sense of their history and accomplishments. That happens because I always put some thought into the OpForce and make sure there are some fun characters in it as well. Lots more fun defeating an enemy that has a name, even if it is imaginary!
