It's going to be tough for existing themes that have a lot of options built in. As one who started to use the customizer in my themes, it's been very easy for me because I've been using the customizer for 2+ years. I can understand the frustration this new direction is going, but I believe this is the right direction for themes that want to exist in the .org repository. Authors do have the choice to not follow suit with their premium themes, but I can only say to each one to realize that more changes will be coming over time.

Perhaps it might have been better to simply create a new repository at .org for "premium free" based themes that offer better design and initiate the new changes and development guidelines instead of trying to change the one that has been in place for such a long time; only to gradually phase it out.

In the meantime, theme developers will need to educate their users and potential users of the why's and benefits of the changes. It'll ruffle some feathers, but eventually over time, things will balance out.