Don't overestimate the need for having both protocols in the same software. Many people are like me: they run both types of clients (I run Xolox and Morpheus currently) and share the same files.

Note that this also means that it is easy to bootstrap the next generation of P2P networks and protocols: just provide any software that rocks and I will share my files there too.

BTW, I suggest that someone looks at Inferno/Plan9 (www.vitanuova.com) as a protocol (Styx/9P/2000P) designed for secure distributed processing and resource access. Inferno runs on top of both Linux and Windows, and has a very nice programming environment with the Limbo language.