Not sure where you got that idea: I use pathogen without involving Git at all.

OK, then you have some kind of shell script to do the downloads, or you do them all manually each time. These are not better alternatives

My ~/.vim is under version control (Git) but not every plugin is available through Git. Some plugin developers use Mercurial, others use Subversion or whatever and most only provide a .tar, a .zip, a vimball or even a single vim script. This Git myopia is seriously getting on my nerve.

it does when you want to have your vim configuration in git. and vundle might be easier then (not, that using git submodules is so extremly hard).