The customizer needs better organization if it's going to be the go-to place for anything more than basic configuration. It will become quite easy to just shove dozens of settings and then the side panel will become very cluttered with no standard hierarchy. Right now with the Widget customizer baked in, there are a lot of setting panels if you have a lot of widget areas. I have seen quite a nice idea for a solution by the team that worked on the widgets that would solve it though.