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I don't understand your objection. It sounds like you're objecting, but
then suggesting an implementation? The line you suggest might just as
easily be present in py3k's default site.py and it would work fine.
As I understand it, "sites" don't need this feature, developers do. 
Let's say I'm working on a typical system with stock python2 and python3
packages installed. Maybe it's a multi-user system, I don't have
control over site.py.
Normally what I'd do to manipulate sys.path dynamically between
different versions would be to install a sitecustomize.py on my one
PYTHONPATH entry that detected the version and reacted appropriately. 
However, writing a program that is both valid python 2 and python 3 is,
as I understand it, both tricky and unsupported.
Will this specific case be supported so that developers don't need to
have root and modify the system python in order to do 2->3 migrations?