We are having problems with our site at answers.unity3d.com because we can't customize the reputation rules.
New users can't post more than one link in a post, discouraging cross-referencing to our software manual, other answers, and other pages on our own domain. That users are discouraged from this is a huge problem! We want our users to post links to multiple resources when relevant!
Rules like this seem to be made to avoid abuse of the site, but we have almost no problems with abuse at this point, and all this rule does is make our users angry and reluctant to use the site.
And why would links to pages on the same domain ever be restricted?
P.S. Bootstrap mode doesn't change this rule either. New users can still only post one link in a post.