Would the following for a 4-player (or maybe 6-player) game work:
Set-up is normal. There is 1 'you are a cylon' card and 6 'you are not a cylon' cards. After distributing loyalty at the start of the game, instead of automatically adding the sleeper agent:
1) Shuffle 2 'you are not a cylon' cards, 1 'you are a sympathizer, 1 'you are a cylon'
2) Seed the loyalty deck with a random card from the deck I mentioned above.
Will this be balanced? I thought it might be more interesting, as it introduces more uncertainty when the sleeper agent phase rolls around, yet giving the humans a fair 50-50 chance that they are safe so that the cylons are not overpowered.