The Alternate Reality is a cliché (and some might say a tired one too), but it does allow us to explore other options and ideas that ordinarily would not be permissable in the course of an ordinary BSG session. Unlike some alternate realities, the ones presented below are complete changes and not cross-overs. While there is no reason to not make them cross-overs (like the 'Mirror' reality in Star Trek), you will have to find your own reasons for making this so!
In this universe, the Cylons have not won the war. Neither have the Colonials. Instead, the war is still raging with no end in sight. With the war is still going, the Cylons and the Colonials are pretty evenly matched. Borders are around the 6400 yahren mark, although combat has raged up and down the lines and they are pretty fluid. Due to this, construction facilities are still operating, and as such, new warships are being produced by both sides, and older designs are also still operating.
This is a slight idea for those who wish to game using the conjectual ships as 'real' ships, with no limits as to what is or is not available. The war could easily last another thousand yahrens in this setting, and while the Cylons probably have the largest empire, they are not the invincible enemy they once were.
What would happen if the Colonials won the war and the Cylons had their worlds bombed into submission? What if a single Baseship and a handful of Cylon tankers and civilian ships escaped, hunted by the Colonials?
This is an interesting one this, however I am not sure it would work out too well though, lets think it through. From a television viewer point of view, the idea couldn't really be taken from the eyes of the Cylons. From what we know of the Cylons from the series, the only characters with any interest would be the IL Series and the Imperious Leader (should he have survived). These are the only beings with any individuality and charisma, but rarely would they go down on away missions and the like (however, that is easily changeable, although BSG does have the sense to not let all senior officers leave the ship at the same time!). So we would have lots of 'red shirts' in the form of all the other Cylons. Because of their nature, there would not be much in the way of the same story lines as Humans, because the Cylons would be fairly logical about things. Centurions would not complain if they had to risk their necks to save their people, and the IL Series would make sure it was their necks and not the IL's! So the interaction between IL's would be the order of the day. Not sure about civilians though, we have not seen enough of them to understand if they have individuality or not - we saw some in "The Living Legend" with the Imperious Leader, but would they be ordinary citizens or special managers? I mean, would just anyone be allowed to see the Imperious Leader on a state visit?
Another point is the combat ability of the Cylons. True, a Baseship is nothing to be sniffed at, but Cylon pilots are not great, and unlike humans, they do not reproduce well. I would imagine a Baseship can not build Cylons (but should be able to repair them), so any losses would hurt. Also as Cylons are not the greatest thinkers, they would have to adapt.
Which could lead to an interesting question - if the fleet believed the Cylon worlds lost, doomed and destroyed, would they attempt to build another Imperious Leader? Would an IL Series step forward to take the job? If they did and later found the Imperious Leader alive and well, what would happen? Could we have civil war between the Cylons? Or would we have a lot of confused Silver Centurions?
Taken from a Colonial point of view, especially the one from the television series, would the Colonials pursue the Cylons? Knowing that they are doomed and certainly no longer a threat to humanity, what would be the point in giving chase? Scout them out and follow with small fast ships sure, but attack and annihilate? Why? Now, though, while that might be the main command view, it certainly would not be the average soldiers view, after all, you've seen your friends killed with no mercy and now Command wants you to show mercy to the enemy and let them go? Pah! So you might see renegade ships wanting to hunt them down.
However, unless something drastic happened to the Cylons - they get a life, wake up and smell the coffe and then realise they can have imagination - I do not see them lasting very long unfortunately.