1. clean url's.
2. content html not loaded in an iframe, but directly injected into the main page, so it becomes indexable by search engines.
These 2 topics are the most important to me. As an addition I like to:
3. have all the separate scripts inside one script to reduce http calls
4. move from the Prototype framework to something more modern, like jQuery or Angular.
So, if there's anybody out there who would like to take up this challenge, please contact me.