Agendas For All
This variant replaces the loyalty deck with some more advanced loyalty cards, similar to Cylon Leader Agendas. With these, however, you need only fulfill half your goals (plus your team's overall goal) to win.
Full rules and 30 new loyalty cards are included below. Please direct questions and comments to the boardgamegeek thread here. I use these cards in conjunction with an extensive but very much in-progress variant, which I will post later. However, they integrate pretty well into any kind of BSG:Pegasus game.