Getting back to the original question:

• Better search mechanism.
• Ablilty to specify which modules a page admin can place on a page.
• Ability for users to have their own pages where they can load some modules(see pageflakes).
• Graphing/Charting engine.\
• And more built-in ajax/atlas support, of course.

In the spirit of the original post, I am going to suggest some significant enhancements (and request for feedback).

1. Enhanced Unified Extensible Installer - to enable Module, Skins, Providers, EditControls for the Property Editor, Control Panels (plus anything that a module developer might wish to install, such as templates for a templatable module).
2. User based permissions - Allow Users to be assigned to permissions (in addition to roles).
3. Personal pages - allow a portal to provide Myspace.com like features (would require (2) above)
4. Workflow - a workflow engine that could allow module developers to define and use "Workflow items"
5. Enhanced Search - speaks for itself

1. User based permissions
2. Personal pages - i'm doing this already in my custom framework but it'd be great if was built into the core.
3. retro the projects to support user based permissions
4. support Web Parts.
5. Workflow.
6. Enhanced search.