It’s smartindent that is messing the comments up, because it’s meant for C-like languages and assumes ‘#’ is the beginning of a preprocesser instruction. smartindent is really only meant to be used if you don’t have a smart indentation file around, and with indent/python.vim you do!

It really isn’t adding anything you need either, it just does some not-quite pythonic indentation around ‘{‘ and ‘}’, and indentation after C keywords like ’switch’ or ‘do’, all of which is getting overridden by the python indent file. The only thing smartindent is still doing is messing up lines starting with ‘#’. Even after editing the indent file in the manner you suggest, I suspect smartindent will still stop you from being able to move comments to the right with ‘>>’.

So just don’t use smartindent on python files. Change the last line of python_pep8.vim to be “setlocal nosmartindent” and your indentation should still be just as automatic and pretty much exactly the same, just without messed up comment indentation.