The problem is keeping up with Intel is a ridiculously expensive proposition. analysis showed Intel's R&D expenditures were $22.1 billion between 2001 and 2005 http://www.emsnow.com/newsarchives/archivedetails.cfm?ID=136... Either staying a few generations behind and building more chips, or buying from the beast seems like the best option.
PS: Intel does manufacturing in china (http://arstechnica.com/hardware/news/2009/06/intel-china-fab...) so they already have access to slightly behind the time manufacturing technology.
I wonder what people are using supercomputers for in the military these days anyway - UAV? Crypto? I'm guessing ballistics is pretty well solved. And you hear the occasional story about suits showing up and requesting that labs disable-in-hardware the execution of Shor's algorithm on their quantum-related tech...