The Python developpers suggest to use 2.x as long as you can, and use the conversion tools to translate existing code from 2.x to 3.0 code whenever 3.0 is ready.
that sure is an interesting take -- if I state I want to use python 3 here and now, will guido come and grab me by the jacket, shouting "use it if you dare!" in that sweet dutch accent of his? ;)
anyway, what I meant was PyMate should include the appropriate flavor of sitecustomize (the current, 2.x-compatible version or the modified, 3.x-compatible version) -- this can be readily obtained by placing the two different versions in two different folders, and inserting the appropriate folder in the PYTHONPATH environment variable.