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Like say you have Catgirl, Thief, and Bro. Well in that game she could have different reasons, or a different way in which she is/became the villain, than if the party had been say, Catgirl, Paladin, Magician. That way you get loads of potential combination, and you can never really tell who's going to be the secret villain until the end, or unless you pay very close attention for clues, and know the characters well.
Alternatively, you could also make the "BBEG is secretly one of your Bros" possibility be completely random, rather than selectable as the opposition. Like say, when starting a New Game, there's a 1/10 chance (or whatever odds) that the "Secret Bro BBEG" gametype is in effect. You don't know that that's the gametype you're playing, you'd have to be on the lookout to catch wind of it. And of course, you'd have the Bro selected to be the BBEG be random, again making it unclear if that is even the gametype you're playing, and if so if they're even the villain.
Only drawback I see, being that including this "gametype" or villain choice, whatever you call it, would be excess amounts of extra work. Probably much more than anyone is willing to do.