I too think the rep system is pretty silly. Maybe that's why you hardly ever see it utilized other places? What you get is a bunch of users giving each other meaningless positive rep points in order to hopefully get one back.
Even without this factor present I still wouldn't take much notice of any given user's reputation. I'm just as likely to take advise from a user with a 0 rep as a user with a +400 rep if I think it will solve my problem.
On the more positive side, it may encourage helpful users to be even more helpful when they are rewarded with a great number of positive points. Also, I assume it helps moderators to identify spammers and what not. If this be the case, I see no reason why the rep system should be removed as it can't really be considered annoying. Ignoring it works pretty well for me.
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