Some of your request are implemented in Adaptable, a new moodle theme that try to break the classic moodle structure.
Add custom pages is easy but adding these pages to the custom menu could be messy. Adaptable has several menus to add these pages.
Add any content in the course page without blocks is really difficult due the moodle layout. We need to use the regions to add this content using blocks. And normally there are no regions in the course page. We are working to add some regions in this page.
Sidebars instead of blocks? I think is better the opposite. In Adaptable you can add information in the frontpage without sidebars, using a configurable grid layout.
And all the modern Moodle Themes could allow the use of the default JQuery elements. If you want to add external elements then you can modify the theme easily.
The rest of requests ar more complex and needs specific development.