Is the only purpose of the '-r' in sys.argv code to 
avoid having to specify arguments multiple times when you're doing 
multiple commands on a line?  Perhaps it would be acceptable to then 
just drop that bit of code completely; having to specify 'register -r 
pypi upload -r pypi' isn't the worst thing in the world, and it avoids 
worrying about oddball corner cases like 'setup.py newcommand -r 
something-different upload -r pypi'.

So, I'd suggest just taking that code out, and then committing the 
patch.