Having the cylon leaders in the game as of Pegasus is nice, but doesn't really fulfil my yearning for the politics among them. So, I'm going to share an idea I had, in hopes that others might add to it, help carry it forward, and/or create something playable.
Aside from other skinjob models as characters, it would include another board... a cylon basestar, perhaps. Also, probably, a set of Cylon-specific crisis cards.
The base star would have a distance track, similar to the Galactica's jump preparation track, but measuring distance instead.
* If the basestar's distance is above that of the Galactica's, it would have some bonus to the cylons, since they can lie in wait for the fleet (perhaps the cylons get to place additional raiders/heavies during an attack), but allow a +1 to early jump die rolls (or something) to represent decreased pressure and more freedom to prepare(even if the space sectors are full of ships).
* If it is less than the fleet's distance, the Cylons are collectively chasing the fleet. This may allow the Cylon leaders to scout the crisis deck from a basestar location, driving the fleet toward unfavorable situations.
The control center location, depicting the Hybrid, would manipulate the distance track by way of a cylon-only skill check (that is, non-infiltrating Leaders, and Revealed cylons only). Depending on their agendas, the Cylons may need to be ahead of, behind or at the same distance as the human fleet. Requiring cards here should balance out the effects of the basestar's distance track, whatever they may be.
I'm on the fence about allowing the basestar board to be targetable by Vipers (and thus having space sectors), but would lean against it.
There ought to be some kind of brig/detention type location, and an admiral's quarters type location, as well. Boxing a line shouldn't be easy or casual, but there should be a way to hinder those of opposing agendas. Since "there are many copies", an airlock (as an activateable location) is pointless. Whatever the mechanic is, it should probably reflect shifting the loyalties of the unplayed models (as well as the centurions?).
Revealed cylons should be able to travel to basestar locations and activate them, although they run the risk of being "contained" by hostile Leaders.
As far as a Succession order for Primacy, I'd lean against that too, barring convincing arguments. Much of Cavill's power was only a result of a close consensus of the the other models.
If there were an alternate way to determine/control the loyalty of a sympathizer, a location on the basestar board would probably be the way to do it. Being able to change the symp's loyalty after it's determined (or that of a revealed cylon!), would have a drastic effect on balance... so that's something to be careful about, although it would be a ton of fun. Cylon leaders absolutely SHOULD be squabbling over the other models' loyalty. Conversely, the other (non-Leader) models have a vested interest in throwing off the yokes, so to speak. It should take concerted and ongoing effort to sway them, if it becomes possible.
This cake would be well and truly iced if the basestar were playable without the human fleet, in addition to being played as an expansion.