"Which expansion" is a tough call.
If you planned on getting both, I would say Pegasus then Exodus…
but if you get only one… maybe Exodus is a good choice. I played at a convention recently where the popular version was base game a Cylon fleet and it played very well. I think one reason at a convention was that no one "walked away" mid game out of boredom from being a pilot (or cylon) with nothing to do - always a danger not so much in a home home <grin>.
You also can added/remove the other elements to change the game up every once in a while, playing with 2 or all three expansion options. This adds to playability.
Beside "the Pegasus", you won't have characters from Pegasus or the skill cards - I am not sure if that would outweigh my recommendation, but probably not.