It seems to me there are three main paths you could take for campaigns in Diaspora:
1. Try to weave your missions into the canon, which is what R1 does (very well, all in all). This seems like it would be the hardest path. As already discussed the turkey shoot and everybody dies nature of the Second Cylon 'War' means you'd be very hard pressed to tell many stories within its framework. But also if you wanted to do missions that follow the fleet you would have to be very careful to justify why these things are never mentioned in the show. The Beyond the Red Line demo was pretty good in that respect. I can't imagine a full campaign that could pull it off however. But then again, the show itself features an entire movie in which BIG and IMPORTANT things happen that go virtually unmentioned within the show itself, so who knows.
I fully expect someone to make single missions based on battles from the show though, at some point. Just seems inevitable,
2. Alternate universes. What if the Cylons didn't do their virus attack thing, or if it wasn't fully effective (imagine a handful of early missions where you play the roll of an unaffected plane having to protect disabled assets until they can be brought back online)? Then there would be an actual war, and one could create a classic 'cog-in-the-machine' Freespace-style campaign. Maybe give the Cylons an actual order-of-battle, with frigates and cruisers as well.
Or perhaps a campaign that departs from the show at some key point (my vote would be for right after the New Caprica exodus) and attempts to give the story a non-retarded ending. I don't have much expectation of this one, it would be a colossal undertaking. But it's an interesting thought.
3. Prequel/FCW campaigns. So obvious it goes without saying. I've thought quite a lot about the potential of this era. Consider that B&C takes place at the tail-end of the war, which means there's more or less total freedom for things set earlier.
How did the Cylons survive against an organized military long enough to start building things like basestars? We know that the colonies became a united force during the course of the conflict. So at the beginning the toasters were probably faced with a scattered, disorganized enemy. Maybe it took the Colonials a few years before they settled on the concept of giant armored battleship/carriers. Perhaps at some point you're assigned to a top-secret proto-Battlestar?
Imagine all the different colonies having different ships, maybe even entirely different orders of battle, at the start of the war, before gradually uniting and standardizing. I bet the poorer Colonies would have brought some really interesting improvised warships and weapons to the fray. Maybe the Viper was an entirely Caprican invention, and other factions had their own fighter designs. The player would start in those retro Mk I's and the II (and possibly III) would be mid or late game upgrades. Seems like the skies the limit from a creative standpoint.
I'm sure all I've done is layout stuff that other people have already thought of, but them's my thoughts, for what they're worth.