Averaging still just doesn't feel right to me, it's hard to explain, just doesn't feel like the winning team is being rewarded at all for winning, but is in fact just making it a lot harder on themselves.
Opting out seems better and it's how they actually do it on the show and probably how I should have done it in the beginning. As for the players with little skill being on the better team. Well for one you won't be able to sit out a player more than one challenge consecutively, and technically, there shouldn't be 'a better team'. Sure a certain team may be better at a particular challenge and have different skill sets, but overall they should be pretty even. I know what you're thinking, but I'm not yet convinced Red Team is the worse team here. They just aren't playing as a team and that's why they aren't winning more in my honest opinion.
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Indie game board: http://www.gamefaqs.com/boards/293-indie-gaming