In 2.5 all html generation is moved from course/lib.php to course/renderer.php so themes can override it. Also print_section() was split into several renderer functions and course formats can use any combination of them. See MDL-36320.
Another major thing is the category/course listings. All courses/categories listings will be under course/index.php, all management - under course/manage.php. Switching between viewing and management no longer depends on global editing mode, so it's less confusing for users (see MDL-37572).
Also course/category listings will also be displayed through renderers and look consistent throughout the site. See http://docs.moodle.org/dev/View_all_courses
Suggestions are welcome!