Well we could go wth the obvious
America vs Iraq...

maybe, play out the american revolutions
america vs british/canada's

civil war?

Now, for fiction
You could go as simple for good and evil a Demon race and a Angel race and give angels like dragons and stuff, demons can have like really cool looking monsters.

Or

For something more appealing
Mankind vs AI....robots go crazy and pretty much humans gotta defeat them or be defeated...been done but I don't think in RTS format.

or

heh, a nuclear explosion in the heart of america transforms a bunch of bugs into zerg (big bug) like creatures, and the rest of earth left in termoil from all the current war is quickly being overtaken, when a third race comes in...god like creatures. toss...