40 answers and counting, so I won't rehash what's been said, and sorry if my point has already been covered and I missed it.

There's a reputation problem on many small sites, but it isn't due to the design of the reputation system. For reputation to serve its purpose, people need to vote. The majority of the benefit of the Q&A knowledge, and the voting that sorts it, is for people finding the information in a search. They can't vote. 

All of the voting is done by site users who have at least minimal reputation, generally meaning they have done some posting that was well-received by the community. 

That's all great in theory. But many small sites have very little participation by users with voting privileges. Few of these people visit regularly. Of those who do, few bother to vote. 

It becomes a viscous circle, where sites get fewer answers because investing the time to write good answers isn't rewarding on those sites. Lack of interest in writing answers and fewer answers by others means less reason for regulars to visit the site often.

For new contributors, it takes so long, and so many posts, to build the reputation to fully participate, that few continue to do so. Of the few who do, even fewer build the rep for community moderation. So small sites atrophy as participation by experienced users wanes and they are not replaced by involved new users.

Reputation plays a key role, but it doesn't work on many small sites because few people vote. Tweaking the algorithms won't fix it, and radically changing it corrupts its purpose. It's a user behavior problem, not a reputation system problem.