Greetings!
We are not actually making a Minecraft clone. I use this example, however, because our game world works the same way, and I have had trouble finding an appropriate system to use (been looking at the options on the asset store). Our game scenes works like this:
In the editor on the back end there is nothing but empty gameobjects with scripts that manage the terrain and game objects. On the front end, the user starts a new game, puts in a seed, and the world/terrain is generated on the fly using marching cubes algorithm, in real time. After the terrain is generated it is seeded with gameobjects (trees, plants, enemy spawners, etc…). I do believe we can use a node based system where the nodes are impregnated onto the terrain at run time. The players can then alter the terrain in real time, build stuff, etc, which also stresses the need for dynamic pathfinding. We wanted to use Fantasy AI 2.0 as this seemed to have both the enemy and NPC AI as well as path finding. However, this, like most of the path finding and AI plug-ins, uses navmesh and is the setup is very static. To wrap up, we are looking for a dynamic pathfinding and possible AI system that is NOT grid or navmesh based, that will work for procedural worlds. A link to the project for your reference is here:
http://steamcommunity.com/sharedfiles/filedetails/?id=136701570
Thank you for taking the time to read this, I hope someone in the community has a lead on a solution for this complicated setup.