There's a lot on my WordPress wish list for the API, but I actually think 3.0 should be almost exclusively focused on WPMU merge. Let's do one big thing, and do it well, particularly since I think WPMU's underpinnings and API calls need some serious polishing.
I'll also go on record saying that a new theme is, in my view, a waste of time. There are plenty of extraordinary themes already out there, and anyone who is serious about their blog isn't going to stick with a stock theme anyhow. Rather than reinvent a wheel that's been "well-invented" elsewhere, I'd suggest a mechanism - during install or setup - to choose from a random series of 20ish of the best themes provided by the community. If we're worried about support for these themes, it's not unreasonable to hold the developers of those themes to a certain set of expectations or threshold of quality to remain on that premium list.
Once the MU merge is finished, I'd say there is a lot of backend / API maturity needed around taxonomies and custom post types before we start worrying about creating a glitzy UI for managing those.
The way custom, non-hierarchical, post taxonomies get handled should be the standard (well, permalink bugs aside). We should be able to define new hierarchical (category-like) taxonomies, and assign taxonomies to pages, and "all the magic" of automatically adding new menu items and new meta boxes appearing on the editing screen should similarly happen.
I envision a similar future for custom post types. Imagine integrating the "add menu" calls with new post type definitions. So that if we define a "news" type, a new menu items (a la Posts or Pages) gets created, with an edit and add new list.
Granted, I speak from the perspective of someone really trying to push the API to the limits (not just a blogger). But I think we really need to hunker down and grow the core API's ability to compete with the likes of Drupal on custom types and taxonomies before we worry about more UI polish, which (with a capable API) can be accomplished just fine with plug-ins anyhow (in most cases).