It sounds like you're basically proposing Plan 9--lots of very small, single-purpose components with one standardized way of passing data between them used across the entire system.

Also, you can ask a lot of people to give up binary compatibility and be okay, but asking people to give up source compatibility and change applications is a much, much harder pill to swallow. Specialized environments (like the syscall-shipping CNK on Blue Gene like jedbrown mentions) are usually seen as something to work around because they are impediments to productivity. A more robust system wouldn't be considered useful if everyone has to start from scratch.