the CPU seems to be 2.5D - 2D plan with vertical register/etc orientation. 3D anybody?
Also, any chance somebody building/exploring non Von Neumann one?
(I am sometimes working on a Minecraft CPU with a MOVE instruction set.)
There's also the fact that the wires transmit information only 15 tiles. It's possible to build repeaters though, but those repeaters have some lag and take up space.
The hardest part are the memory cells. A single bit, even in the optimal configuration, takes up 3x3x2 blocks.