I actually like that the preferences are stored in JSON. This is one of the features that pulled me in to Sublime Text.
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.