[johncoltrane]

Pathogen and Vundle have different purposes: one could be called a "runtimepath manager, it injects the plugins found in ~/.vim/bundle into Vim's runtimepath like if they were installed the standard way, while the other is really a "plugin manager", allowing you to update, install, delete, deactivate plugins.

Because they have different purposes, they must be compared according to your needs.

I don't need a "plugin manager" but I like my plugins to be organized cleanly so I use Pathogen.

If you need something to help you "manage" your plugins, Vundle is a sensible choice but you should compare with VAM or neobundle.

In short, comparing Pathogen and Vundle makes no sense: compare what's comparable.