Vundle is strictly better unless you automate your software updates and want to be able to update your vim plugins without having to launch vim to do so. Pretty tenuous but maybe some sysadmin-inclined people really prefer this.
Vundle has proved a significantly better system for keeping things managed and uses the exact same approach and code as pathogen. It's hard to criticize vundle and support pathogen since they are so similar.
vim +BundleInstall! +qall
Vim still opens but could be useful if you're trying to automate vim somehow.