The reputation system was introduced with the promise of being developed over time. Unfortunately it was left low on the priority list as long as it solved the main issue of spam. Personally, I would like to see upvote/downvote no longer impacting reputation and having it instead based on your followers and how much SP they are collectively backed up by.

With that, I would also like to see this number used to incentivise giving a boost to users with lower reputation.