I think the reputation system works pretty well, I've been around for a while and read the forums for 4 years, but never got around to actually signing up and replying till now. There are always a few problems with any system but I think this one works as good as any other. Chief Delphi has done a good job of creating a great community and a place for us all to share thoughts and ideas and also some other things that can't quite be considered a full thought.
I'll stick with it at least through college even if I'm not on a team anymore, despite the reputation system or anything else that might have some minor flaws.