I think the easiest solution would be just to let pathogen handle your runtimepath for you.
pathogen#infect()
can take paths that specify different directories that you can use for your bundle directory.
So if your .vim
directory would look like this
.vim/
autoload/
pathogen.vim
bundle_python2/
<plugins>
bundle_python3/
<other plugins>
Then inside one of your vimrc for python 2 specific stuff you would have
call pathogen#infect('bundle_python2/{}')
and for python 3 specific stuff you would have
call pathogen#infect('bundle_python3/{}')
Since each plugin folder is really just a .vim
folder you can place your python specific configuration stuff in a folder of the corresponding bundle and pretend its a .vim
.
This structure also has the added benefit that you can change both configurations at the same time if you feel like it by putting common stuff in .vim
normally.
You can also pass multiple bundle directories if you feel like to pathogen so you can have plugins that are shared without duplicating files. You just do this by passing multiple paths to pathogen#infect('bundle/{}', 'bundle_python3/{}')
After this is all done you can just create aliases for vim to call the correct vimrc file.