I know it's a massive amount of extra work and removes a lot of the simplicity of the script but a loader.php file with a template system would have serious advantages. If you think that a DDL site only updates about once a day when the queue is processed by the admin it provides the perfect opportunity to cache the most used pages like the index and main $type pages.
Caching additional stuff like the stats in the sidebar, top downloads etc would also then be a lot easier.
Not much of a benefit to smaller sites but a considerable difference to larger sites.

Still though all sounds great and looking forward to testing it and creating modules.