I switched from Pathogen to Vundle, at the prodding of people on HN, and I can't say I am all that thrilled about the difference. It basically does what Pathogen does, plus it does a bit more. The issue is that the "bit more" that it does just doesn't seem... polished.. to me, and covers things that I never found troublesome to do manually anyway. I'm not going to switch back (since it does what Pathogen does there isn't a reason), but I don't think it is better, just different.

1. I switch to another tool if and when I have problems with my current tool. Because Pathogen has served me well for the last two years there's no reason to switch to Vundle or some other plugin manager.

2. Vundle is too heavily Git/Github-centered for my taste.

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.