Now, I'm not going to repeat the-endlessly answered-"HOW MANY LE FACTIONS ARE LE THERE GOING TO LE BE ECKSDEE!1!" question. Instead, I'm going to ask about the possibility of factions that are identical in every statistical way, but differ just in looks. Like maybe a different type of robot, Cybran diagonals or Aeon curves to what appears to be the UEF boxes, or maybe a completely organic race, a la Tyranids or Zerg.
it takes a lot of time, effort and money to do this and sort of defeats the purpose of saving money by making a single faction. maybe they will in the future
and the biggest waste of resources if it is just cosmetic. At least from my perspective, if something looks distinctively different it also should be different in role/behavior/whatever (in RPGs "for story reasons" might have some justification as cause for a different style, but even there it's mostly a case of avoiding too many balance issues )
i think there's room for microtransaction unit skins and animations. i'm not sure to what degree that was discussed but i wouldn't think it unimaginable given there's already variations of commanders planned. over a long period of time these unit skins could add up to a premium cosmetic faction which is something the OP might like with proper execution (read: ethics) such that gameplay is not affected and purely cosmetic microtransactions allow users to support a game they enjoy while not being put off by unnecessary nickle and diming. same goes for premium DLC which boosts short term profit at the expense of the long term.
like all the others have said above how ever im quite sure factions and stuff will spring up all over the place when the modding community gets their hands onto things.