I really love the speed at which useful relatively bug free features are added to WP. For 3.0 my preference would be a focus on the WPMU merge. I look forward to the possibilities it might bring and would encourage you to look at the additional domains issue others have mentioned.
But if the dev team are looking for core blog features my vote is for, easier internal linking to posts and pages from the post editor (and page editor too I guess). As this would greatly encourage internal linking (which is good practice for user interaction and SEO). I would suggest also adding an option to ignore *internal* pingbacks.
This is one feature I think would make blogging easier and quicker. I think WP dev should not forget this even if we move to more CMS type functionalty.
