The problem isn't so much in architectures, but in silicon processes. HomeCMOS (http://homecmos.drawersteak.com/wiki/Main_Page) is notable in being the relatively rare project to look at this layer in the computing stack at all.

Once you can do your own processors, the architecture is alright. To avoid running into licensing issues all the time, projects like RISC-V (http://riscv.org/) can help - or open cores like Leon (SPARCv8), OpenSPARC-T1/2 (SPARCv9), openRISC and several more.

The problem is, the silicon processes were optimized for investment heavy, large scale operations. To ensure the livelihood of general purpose computing we need a "3D printer for logic gates" (for lack of better term), even if it's economically and technologically less efficient (but not too much, obviously).