Ability to use things like BookOrbit (or alternatives) to manage your books and sync your progress/stats
I discovered BookOrbit about two months ago. I think that it, together with the KOReader plugin that exposes the remote BO UI, may turn out to be a game changer in how I organize and access my ebook repository.
Same here, I jailbroke my kindle just 1-2 months ago (when the PW5 JB came out) and I had been using BookOrbit for only a few weeks before then. Since then I've read over 15 books and been loving BookOrbit and KOReader.