ist an amazing idea. seriously. but im not seeing much balancing. if you plan to actually make this a game, not just a fanfic, you really have to think about balance. there are two types of balance: analogue and complex. analogue balance is found in most early RTSs and games such as classic Doom to Heretic. complex balance if found in just about every modern RTS (except for StarCraft) and many modern shooters (Halo 3 and Gears 2 are prime examples). analogue is easier to do, but not as intersting, whereas complex is the reverse.
also, you seem to be jumping straight into it. your putting alot of thought into it, but perhaps too much, like thinking too far ahead. what works for me is to come up with most of it along the way. in my fanfic (posted up here and will be updated soon) i just made a "brief" plot outline and made a list of major characters. the rest i come up with along the way. the same happened in my other fanfic (which may or may not be posted up in the Absent Without Leave Discussion, but is definately on the SPPf).
i know your not me and everybodies ideas work differently. im simply just making suggestions to help make it even better. but you really are on to something. although i lack skills in modding and game design, i am able to help write down a plot and even do artwork (except for environments). i can help, but only if you want it.