God, I love the series and everything, but the ante comments on this thread border on fanatical. Why not turn it into an RTS? Because it would lack traditional elements? Because the humans wouldn't be able to use tanks? For crying out loud, have you all been sat at home playing Command and Conquer for the past fifteen years? Times have changed, and many RTSes have adapted to include originality. People are reciting and singing the praises of X-Com sentiments and gameplay, when they really mean Company of Heroes!
Want an example of story in an RTS? Go look up Age of Mythology - a campaign which took days to finish, which told an epic story of love and loss. If Half Life's original expansions got away with telling the stories of washed-up security guards and Black Ops agents, then surely an RTS can take an equally different alternate route through the story, right? Or would that be 'uncanonical'?
Furthermore, there seems to be little problem when it comes to faction balancing. Sure, the Combine devastated Earth's forces within hours, but that was only the initial invasion force (personally I feel it would be quite interesting to have to retreat through such environments under attack by the Combine, but that's beside the point). What remains on Earth (with the portal now closed, too!) is little more than an expedition party in comparison with the other aspects of the empire. Thus, considering the humans are capable of building huge rockets and nifty anti-Combine gear (see: Magnusson's rocket/device) then the playing field is relatively level, given some artistic license. Furthermore, a great and artistic third faction could be made out of Xen's creatures.