* Even better extension support -- enable writing extensions in any language: expose a file system based API for a full Unix philosophy experience. uzbl has something like this but it's not nearly as ideal as Vimperator is for my use case.
* As others mentioned, lose mandatory UI downgrades and other crap Mozilla's been pushing us lately: give us a platform to customize instead. (Practically running a Firefox compiled from sources helps with some of the issues people have, but sadly there will be a day they overhaul the UI in such a manner it hinders the usability. And because of the security stuff I just can't go back and use an old one forever.)
* Yeah, better bookmarking. Firefox could use a better system, and Vimperator doesn't solve it either. Full-text search among history + bookmarks would be pretty good.
The well exposed API for external apps could solve it all, save for crap UI. For instance, the bookmarks could be crawled to an org-mode document where I could annotate, categorize and tags things to my heart's content.