With the the release of 3.6.x all Theme Plugins were broken. As the top 3 themes have over 32,000 downloads it would seem to me that there will be thousands of very upset admins, that updated Moodle without realizing Moodle HQ provided no time for the theme developers to update PRIOR to Moodle 3.6 going live. A week after the release of 3.6, none of the top 3 themes have been able to sort out all of the changes made to Moodle so they can publish updates. IMHO Moodle HQ needs to collaborate with the Theme developers before making changes to how Moodle works. In a rather long thread discussing the future of Moodle Core and Themes it would seem to me that the core coders and those developing the most popular themes should talk.
That said, why not take a page from other platforms and build a layout designer that allows the end user to layout pages as they see fit, Widgets/plugins can be added where ever needed, course pages could be a little more structured, however a Yootheme Page Builder approach would be awesome. Designers could save layouts to a central repository, same with widgets/plugin, all of which can be accessed from the Page Builder rather then need in to navigate away from the LMS to Moodle to do this.
My complaint with Moodle is the way pages are laid out. Content and sidebar. No easy way to change this on course pages. The main menu is also very late 1990's, it needs a menu manager that can be customized easily.
I see the core and theme as 2 separate entities, however the 'core' needs to be built in a way that allows the Theme to be creative and without all the restraints the current model imposes. An update should not break drop down menus, and if it does the update should warn the user about potential issues before updating. In this case the 3.6 update should have stated explicitly "WARNING IF USING A 3rd PARTY THEME. DUE TO EXTENSIVE MOODLE CHANGES, AT THE TIME OF PUBLISHING MOST 3RD PARTY THEMES DO NOT SUPPORT MOODLE 3.6. PLEASE CHECK WITH YOUR THEME DEVELOPER BEFORE UPDATING TO MOODLE 3.6 AS YOUR SITE MAY NOT WORK AS EXPECTED AFTER UPDATING TO 3.6. WE APOLOGIZE FOR ANY ISSUES THIS MAY HAVE CAUSED."