I would just like to be able to manage and version control my own packages...
Pathogen basically makes the plugin path recursive, so you can nest and manage plugin files, Pathogen + git allow you to manage all of your plugins in a centralized config location via submodules.
I mainly don't want use package control because it relies on a centralized database of plugins. Not all useful plugins exist within this database, and what happens when that reference goes away?
I would much rather be able to add a Package path for instance, that seems reasonable to me. To simply in my user prefs say, "Hey, also look in this directory for packages."
So for now I'll just have to symlink everything into /Packages... huge pain.