Okay, I think this could work: Have a specified area to originally build up your camp base thing, and 'expander' buildings to expand the area. Also, to prevent turret rushes *cough*Star craft*cough*, maybe the expander buildings could also have specified areas.

Another Idea: instead of URF as a new faction, how bout covie seps? 

My idea was that you had an area were you could build your Alpha base and then their were firebase/Citadel slots on the map

So...instead of having UNSC vehicles...have cheap second hand, stolen UNSC vehicles? (URF)

Same with Covies?

I would really enjoy a completely free base design.

Though I believe IF flood were to be added as a faction...their base design should be more like the current one but only with a gravemind. You could make infection forms...and depending on what your enemies...(or you could add an option where your friends could give you units for your own)...you can infect them and form your own troops.

From the gravemind you can purchase special upgrades (improving infection forms, income rate, etc.) Eventually if you get enough biomass to donate to your gravemind (Note: You will have to sacrifice your units for the biomass). You can buy add-ons for certain productions buildings (while uncanonical, I know, it's practical for an RTS.

The currency for the flood would actually be biomass. So...if you really need the money. You can add your weaker units into your gravemind for the chance to get more biomass quicker for better units.

Summary: I think that there should be more factions...each with a few unique features on their build order. And that the flood should be like the Halo Wars build order.