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.
I previously used pathogen + git submodules .. It was very challenging to manage and much harder to keep up to date.
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.
Yeah. I'm just citing the only reason I've heard, which is that invoking vim just to update a plugin is gross. Which is kinda true - what happens if your vim config is in some bad state and doesn't start properly, your update process breaks unnecessarily (odd coupling to have). Definitely edge case-y, but a tradeoff anyway.
