Let's say for the sake of argument that there are 6 big bases circling the system, for example:
* 3 large stations in orbit of planets/planetoids
* 3 pirate style stations
And 15-20k in from each of those systems is a smaller outpost, connected by a short trade lane. So 12 dockable bases in total.
Each system owning faction (of which there are currently 4, and therefore space for 2 more in this example) can claim one large base, and the accompanying smaller base. A typical battle would involve 2 opposing sides with the base setups mentioned above, and involve the attack/defence of each. A battle would unfold like so:
The smaller base would have to be attacked and conquered before any assault can be made on the larger one. Conquering the smaller base is achieved by killing or driving off all defending forces, leaving the base surrounded by nothing but the entire attacking force. The attackers then win the right to dock at the conquered smaller station, while the defenders are forced to dock at their larger one. Then the battle is repeated at the larger station. Obviously there would have to be an agreed respawn limit otherwise the battle would be endless.
An alternative idea, is that each side is limited to one Battleship as their flagship. Once the flagship is destroyed, that side is forced to retreat one step, ie: flagship is killed while attacking enemy small base, flagship has to then defend it's own small base. Flagship is killed again in defence of small base, flagship is forced to defend large base. Flagship killed in defence here, then that side loses.
Anyway, that's an idea of how a skirmish map could work, it's by no means flawless and I haven't explained the possibilities available when a side also has an ally to fight alongside, but I'll leave the speculation open for the moment.
Of course, I don't mean to steal any limelight here, this skirmish map idea would be the perfect ground to implement a lot of Dab's original ideas without upsetting the rest of Discovery, especially the base building. My only hesitations are that the base building by way of patches would mean periodic updates both client and serverside, which isn't ideal.