If you do that idea how about you go for an AU rather then canon NBSG? Have the colons splinter and players vote between building for the colonies, the Bio-cylons and the Free Cylons.
I thought about Battlestar Galactica: Deadlock, so put it in the first Cylon war and give it a try from there.
This is a total segue from the topic of the quest, but personally playing
Battlestar Galactica: Deadlock frustrated me enough that I returned it on Steam, despite enjoying it at first. It was a very solid space RTS on its own merits, but felt a lot like someone had designed a solid Space RTS, and then slapped a
Battlestar Galactica themed paintjob over it. In particular, a core aspect of nBSG was that the Colonial fleet used large flak barrages to stop Cylon missile barrages and bombing runs from Cylon raiders, whilst Vipers dart in and out of the "fortress" provided by their parent ship's firing solution, engaging their larger Cylon adversaries. This means the Cylons and Colonial fleet operate in very different ways, producing a really interesting combat paradigm.
In
Deadlock, fighter operations and flak barrages from your Battlestar exist, but they feel very tacked on - the Galactica-type Battlestar is one of the
only ships which can do it - and they are not core elements of play. It's possible for your own flak barrages to hurt your fighters, which goes against the whole stated point in the show that Vipers would know their parent ship's firing solution and avoid it. Also, Vipers cannot carry ordnance or really do much of anything other than shoot down or be shot down by Raiders, or damage other small ships with gunfire. This makes the whole decision to orient the fleet around omnicapable carrier-battleships seems a bit odd if the air wing - the primary arm of decision for a carrier! - cannot strike decisively. This is contrary to the show, where Vipers are often tasked with acting offensively, carrying, missiles, bombs or even nukes to eliminate key targets.
To be entirely clear and fair here,
Deadlock had its own quite well-designed and fun combat system. From what I recall, you had to trade off doing direct damage against armour, the ship components underneath or systems damage via hacking, and ships could use guns, missiles or even lay mines, and it played really well from my experience of it, with both fleets performing differently. It seemed like a pretty good game! But it did not feel authentically nBSG to me, and that was why I originally bought the game.
What I would want from a
Battlestar Galactica RTS is Battlestars operating as flagships to task groups of various more single-role ships - little escorts with lots of flak guns and maybe some pocket carriers or gun and missile boats - against Cylon fleets which are all about spitting out waves of ordnance. Carrier operations including sending squadrons to do jobs some distance from the carrier would need to be a core part of play for both sides. The Colonial fleet would need to rely on an integrated defence based on combining flak barrages until they can strike with either their Vipers or force a decisive gun battle, whilst the Cylons should be all about hit and run attacks, unpicking Colonial defences, isolating individual ships and destroying them with multi-vector attacks which overwhelm their defences.