I think one of the obvious changes that can be made is drop the reward for accepted answer to 5 instead of 15, also probably increase a negative impact of a downvote vs an answer for both the answerer and the downvoter to 3 and 2, I think, to discourage blind downvoting of anything that at least looks like it can help and to encourage people to write a little better posts, say with an explanation of how this code works, even if it's repeating of what the code spellsrepeating of what the code spells. Probably also add a 1 penalty for an upvote [update: to answers only], so that you're not just sharing a "like", but are also giving a bit of your own hard earned rep to encourage the one who gave a good answer to make more. This change, while small, will drastically overhaul all the rep hunting strategies, as the numerous cross-upvoters will likely get uncovered and eliminated, and blind accept-spam won't provide as much rep income as before.
Still, whatever people will do with the rep system, munchkins will accomodate to it and probably get on top again, and any impact here can discourage many people from participating in SO or SE altogether, thus any measures of this kind should first get weighed against the probable community impact.