Custom settings screens are no longer going to be allowed in WordPress themes submitted to WordPress.org. All settings are to go through the Customizer now, after a theme review team meeting in Slack today, where the change was championed by Justin Tadlock.
Tammie Lister has more information and links to the chat on the TRT blog, and they are going to have a series of posts come out to help folks move their options into the customizer. One interesting tidbit is that previously submitted themes have six months to move their options as well, though there is no set strategy for enforcing the timeline.