hi i have done similar terrain as minecraft-like and marching cubes voxel based and normal height based based projects, in unity and gamestudio , i can only stress that your approach is on the wrong track , in the case where you wish to represent a lot of models /entities as fast as possible ,each entity must be rendered and that is way to much , you must fake it by joining the meshes or creating/building up a single mesh to represent all the cubes visible faces such that it takes only one mesh to be rendered instead of thousands ..

http://forum.unity3d.com/threads/wip-john-doe-yet-to-be-named-project.393060/

you need to research why and how.