This post at Dev4Press outlines what MillaN, its author, thinks would be a necessary addition to WordPress.
Based on the comments, it appears that a lot of people agree with this list. Some of the items mentioned can be achieved with plugins (e.g Tax Meta Class to add meta data to taxonomy items, Custom Post Types Relationships for, well, creating custom post type relationships), so expect there to be a bunch of debates about what should and shouldn’t go to the core.
I like his list, but I disagree with his assessment that we don’t need new core themes. We do, especially to bring about the standard for how a theme options should be designed. This is the aspect that desperately needs to be standardized. Different theme companies and individual theme designers have their own idea of how the theme option UI should look, and it’s hurting the users.