Back in the day, I ran a BSG style campaign for a bit. I made up a fleet of about 100 ships, put the players in a Gazelle Close Escort with doubled-up crew due to the fleet overcrowding and put them to work scouting possible routes for the fleet. It became a basic exploration game with the occasional Cylon thrown in.
The hardest part was realistically using the Traveller Jump Drive with the need for advanced scouts. Coordinating when and where the various scouts would meet up to provide intell to the fleet was a pain in the posterior.
Think about it for a minute. You need to look at EVERY system that you might go to before you got there then report back to the fleet where they decide which system to jump to then you have to do it all over again for the next jump. By having the Cylons only be a few jumps behind, it really put the pressure on the fleet to keep moving.
It was fun for a while. I fell back on the Long Night scenario to give them something to find in most of the systems, but I ran into the problem of what to do with all the humans that they found on these worlds? If they left them, the Cylons would wipe them out, if they took them with them, where were they going to fit 200,000 TL 4 primitives in an already overcrowded fleet? I tried using alien "Humanoids" but that didn't seem to work very well either.
Using the new BSG, it might not be too bad. There would be a lot less "Planet of the Week" type of games and more internal Fleet Politics.
I would still recommend that you give the PCs there own ship, but double up all the staterooms and push the supply issues. The other people might be totally worthless for the operation of the ship, but will make great adventure seeds. Barbers and Socialators aren't much good at running starships... Obviously the fleet has to skim in every system they can. I figure the fleet probably moves 1 parsec per Month under normal circumstances.
Be careful about getting the fleet backed into a spot where they have to make 2 jumps without refueling, it is almost impossible. Remember, probably 75%-80% if the fleet will be Jump-1. The original 12 colonies were all habitable worlds within J-1 of each other; that is why they were settled.
Pocket Empires might be a good source for figuring out what they will run into.
OK, I will stop blabbing now. I really liked this idea for a Traveller Campaign though. There was something engaging about taking a misfit fleet across a large area of space to get them to Earth. Of course, at some point you will have to decide what Earth will be like...