Why is fabrication of ordered graphite substrates difficult?
Graphite is a semimetal, and no more mambojumbo than with metals, but it doesn't do anything with the problem. 
Silicon/silica can be melted, purified, doped, can single crystals grown, can oxidize the surface, making the silicon semiconductor an silica insulator. By "can" I mean that engineeers know well tested methods, optimized for half a century.

Graphite cannot be reasonably melted, cannot grown to single crystals, cannot doped with similar techniques, highly anisotropic, so cutting maybe an issue, and when you make thin layers, it is hard to oxidize in a controlled way to make an insulator out of it. The resulted oxides are semiconductors, and there is a large variety of local structures that can appear with different electronic properties. By cannot I mean that no one really though about these problems until the last decade, so there might be equivalent solutions with e.g graphene, nanotube or other nanocarbon structures.