Ships for combine could include the vast bizarre array including the walkers, etc. Ships for the humans could include "dog". Would certainly be a unique take on what is, by far, the best FPS ever created (truly a masterpiece, even though I usually abhor FPSs--if you haven't played HL2, believe me when I say it's spectacular!).
The mod has merit, though it would take a lot of fleshing out for balance. Basically on the human side there would largely be heroes (Alex, Gordon Freeman) while the combine is a MASSIVE presence with little intelligence. From a RTS point it would be a big challenge.
Just my $.02.