Pathogen loads plugins, but it doesn't manage them. Neobundle lets me list some plugins in my vimrc and it'll take care of installing them, updating them, and even only loading them on filetypes where they're useful.
Pathogen does none of that and I find every one of those features useful. One of the big ones, honestly, is just the simplicity of listing a new bundle in my vimrc, syncing it to all computers, and having it deal with getting it. Much better than syncing large git repos across computers.
pathogen loads the plugins which is all I need. Does Neobundle do something else?