Just sandboxing what changes themes can make to the behavior of the system would be a win. As far as WordPress is concerned today, there's "themes" and there's "plugins", but there's no separation of what those two things can do -- plugins can change the site's look and feel, themes can change how the site (and WordPress itself!) works. As far as WP itself is concerned they're both just big bags of PHP code that can do anything PHP can do.

That leads to all sorts of debugging fun when something weird is happening, and opens up naïve users who assume that a "theme" is somehow safer than a "plugin" (because all themes do is change the look and feel, right?) to security risks from downloaded or hacked-up themes.