I have noticed that most resources in this game are finite. A lime stone deposit only goes so far before it’s not quarry-able. Granite boulders are about 25 rocks and they are dead and are finite in nature. Trying to hunt individual rocks even with all related skills for finding them is very time consuming and boring. This is a big issue in an MMO since in the long term people’s locations will no longer be viable. While hauling from further and further away is a short term option even that will no longer be viable for long term sustainability. Overall this is a serious issue and I am sure you’re working on ideas to solve it. I have a few that may help.
Mines:
The best so far but I think you should have the option to go down deeper once the first layer goes out to far since that is the nature of mining.
Granite, Stone, and Lime:
Granite needs to have a quarry-able area like the other two.
All of these resources should have an Advance skill for each type that will when combined with prospecting, quarrying, and levers and pulleys (as prerequisites) will allow the player to find and construct a quarry pit. This would function as a mine but be larger require more resources to build etc. What this would be aimed at is towns are small-medium groups of players. This will also leave the existing quarry areas as a starting resource while moving into This Pit model for longer term sustainability. I chose these skills as prerequisites as that you need them to Find, Dig, and Raise to the surface said resources.
Trees:
Make most every type plant-able I don't care if it takes a week or month to mature (though some could be faster than others). Related skill Arborist will speed it up since any one can plant a tree some just can do it better.
These ideas are a start but the issue is still there even after a year of playing there will still be problems in any given area. While a better transportation system will help push this out further you are ultimately looking at the need for a better regenerative resource model I suggest EVE as an idea for potential models since they have one of the Player driven market I have ever seen.