So, a week or so ago, our group came up with a couple of variants that spiced up our BSG games quite a bit. We wouldn't recommend these for new players, but it's an interesting variant.
Basically, the idea is that everyone gets one of the Cylon leader agendas, which is their personal victory condition. In a 4 player game, 1 person has a "Cylons win" agenda, and in a 6 player game, 2 people have "Cylons win" agendas. There are two ways we did this:
Build an agenda deck with the proper number of cards with each team winning. At the start of the game, each person gets one card, which determines their loyalty for the game. We also gave people two loyalty cards so that if you saw someone's loyalty cards you knew which team they wanted to win. (This needed a referee who wasn't playing, and the "Cylons win" player had one "Not a cylon card" to help them hide.)
Everyone gets one agenda of each type at the start of the game. Deal out loyalty cards as usual through the course of the game. If you have a "You are a Cylon" card, you want to achieve your "Cylons win" agenda. If not, you must complete your "Humans win" agenda to win.
We liked option 2 better, since one brilliant part of this game is not being sure what team you're on at first, and option 2 preserves that. Both options made for really exciting and interesting games, albeit ones that were quite different than usual. Resources tend to decrease steadily, but usually across the board - the humans don't tend to lose on one resource being really low, since Siege Warfare and Convert the Infidels are probably floating around somewhere. Also, peoples' actions become really inscrutable - is that person who tanked the skill check trying to kill us or just complete their agenda?
One downside is that the tension tends to get backloaded a little bit - for the first part of the game, you lose 2 or 3 of every resource and everyone's happy about it. It also introduces some game-i-ness that people may or may not like. For example, if Galactica is damaged 3 times, you might leave the damage on there as long as you're not worried about getting blown up. Then the Cylon with "Salvage their equipment" will fix it for you, or at least won't be actively trying to kill the humans until it gets fixed. In some ways, this is a nice balancing mechanism - since resources tend to be lower, there are more opportunities for the humans to lose off a choice on a crisis or a jump. Being able to minimize the number of people who would make the "humans lose" choice is good for the humans.
We also made some tweaks to the system to make things work. First and foremost, no Cylon Leaders, no revealing, and no Cylon locations. We mainly did this because we felt like the Cylon Leaders needed some tweaking to work in this game (skill card draw especially), and we wanted as few variables as possible at first. So we want to work them back in once we get some tries of the variant under our belt.
With no Cylon locations, how do you get Super Crises? Well, every time to go to a penalty location or get executed, you get a Super Crisis. But, you can never play more than one Super Crisis in a game. This makes a player with Mutual Annihilation not so obvious, since you get Super Crises relatively often, and often without your control.
Lastly, every player is considered to be a revealed, infiltrating Cylon at all times. This means Treachery cards are usable by everyone. The only downside is that they don't get drawn all that often, so they become less prevalent, and Reckless skill checks are less of a worry. We get the feeling that the humans need some help, though, so I don't think that's a big issue. Also, since you've already revealed, you can't reveal as a Cylon (and where would you go?) If you get executed, you just chuck your hand and get a new character.
We've yet to try this variant with 5 players, but we think the teams should be 4-on-1. I think there's a lot of tweaking to be done with which decks the agendas should come from or if they should just be totally random. With 6, of course, they all get dealt out.
Anyway, there it is. It's a work in progress, so if anyone has suggestions on how to work Cylon Leaders/Locations back into things, we'd love to hear them.