So an idea I've thrown around for a while now is moving natural wonders, but with this post I would like to put a bit of a twist onto that idea.
So basically after you harvest the rare resource you would have choice. You could either "destroy" it for another resource immediately, or you can keep it around to harvest it again in the same spot at a later date.
Destroying the resource would 'set it free' and it would spawn somewhere else in the wild with its usual regen timer. Keeping the resource around after harvesting it would result in double or maybe even triple its regeneration timer. If the resource is harvested again after that longer timer, the timer will become even longer than the last time.
I feel that the timer would be punishing enough that it wouldn't be worthwhile to wall in and hold down the resources anymore, and I feel that the destroy reward would be good enough (in my opinion) that most people would just destroy the resource instead.
These changes would still give the players the ability to lock down resources if they wanted to, but it would strongly discourage that behaviour.