Use vundle instead of pathogen - it installs the plugins for you, so managing them in source control is much easier. Lines in a vimrc are much less of a headache than git submodules etc.
> Lines in a vimrc are much less of a headache than git submodules etc.
I disagree. This may be true if you don't understand git submodules, but git submodules are not hard to understand with just a little effort. Once understood, git submodules are very easy to work with.
Also, this may be just a personal quirk, but I'm not very fond of managing vim from within vim. It would bug the living daylights out of me to load vim just to update my plugins. I'm probably the only one who feels that way, though.
