I'd love it if they were stored in dotfiles (something I like about Textmate 2), but at least all your config gets stored in a nice User package.
Actually, things are stored in a few directories. It took a while to figure out where Sublime stores everything so I could write a dotfiles script for it.
Having to set things up through Package Manager is a pain. Not sure why that's the first step whenever I read an article on Sublime. A simple package file script that git clones/pulls plugins is more maintainable.