Step 1... Create a character creation branch for Galactic Conflict. It would work like the foundry slot worked.
Bring a new server shard online and name it DogsOfWar.
Galactic Conflict option would only be turned on for that shard.
All characters created would be faction 0. When queuing up for a battle, total earned pestige points would determine which ships and what gear are possible. The mission briefing will indicate the opposing sides and what the objective is for each side. Based on this info, the players will decide which side they want to play.
That decision will set faction 1 or faction 2 status for the duration of the battle.
One side will almost always be an antagonist group from the core game. Terran Empire vs Federation. Etc.
Once new PvP system is working as intended, on the main server, switch everyone to faction 0 after revamping the core game to no longer even reference the 2-faction system. All players would be Alliance.
But the PvP shard would be all about the different conflicts from all eras of Trek... Even the Romulan-Earth war...
Just a thought...
When it comes to MMOs, I wear prescription glasses. Whether or not they are rose-tinted is beside the point.