I haven't played with the new robot control system (last robot I worked on was 2007) so I don't know much about WPILib, however from the non hardware side of things, If your going to be rewriting the library to not be platform specific perhaps you should write the platform specific stuff in a platform independent library (only do the work once).
I realize that it adds another library that would be needed for development on any particular machine, but as example
http://qt.nokia.com/products is a platform independent C++ library. There are versions for linux, and VsWorks and there are two different opensource licences that it can be used under.
just a thought,
--Alex