The Thousand Yahren War is the standard setting for this BSG site.

The war with the Cylons lasted roughly a thousand yahrens, and while ultimately it was a dramatic defeat for the Colonials, that did not mean that it was always like that.

During the war, every conceivable type of battle was played out, mainly due to the fact that the Cylons wanted the extermination of the humans, and the humans were desperately trying to avoid this. Thus battles were Battlestars versus Baseships, Baseships relentlessly playing cat-and-mouse with wounded cruisers, fighter ambushes, deep range strikes in the heart of the Cylon Empire, convoy escort/destruction missions, fleet battles, basestation destruction raids, ground base extermination and many, many more.

The Colonial player should devise a fleet (of any set amount of points - some of the fleets were truly huge, like the Fourth Fleet, which consisted of some 600 vessels), and the Cylon player should get the same amount for Baseships and their variants, and then go for it!
A typical Campaign map can be used with little modification, although destruction of vessels and bases will be happening on a much larger scale.

The key is to give each mission a goal instead of just 'You detect the Cylon Fleet and decide to attack'. These types of missions start to get boring real quick, and with the limited amount of ships present, tactics for knocking out certain types of ships become all too easily picked up. However if you suddenly have to rescue a high ranking Colonial official from a wounded Baseship which is about to receive reinforcements, then the game becomes a lot more than a simple shoot them till they drop scenario.

Setting the date of the war also limits the type of ships being used, although if playing during the latter half, then the Colonials might start pulling early Heavy Carriers out of storage (or museums) if the battle starts going against them too quickly!

Just remember that the Cylons are not evil. Yes, they did/do commit atrocities as we would view them, but they did not start the war - the Colonials did. The Cylons just finished it in a most efficient way.