I don't know how much of this is implemented in RC2, but here goes.
1: Separate imagesets, scriptsets, stylesets, languages, and the themes themselves rather than being forced to use multiple copies of an image, stylesheet or script, just have a single set where this is desired.
Imagesets would function a lot like smiley sets do - being called from smfdir/Images/set/... rather than a subdirectory of themes.
Stylesets and scriptsets would function a bit like MyBB's css loading does. Rather than have the theme call these files directly, the theme instead has a list of available files that it can call, and if a given file should apply to a theme, it is selected directly.
Languages are simply text entries that should be called directly, there should be no need to call them on a per-theme basis, ever.
2: List items should be defined in settings, not in the script or in the theme - for example, BBcode, IMs, profile fields (including the entire postbit), and the menu bar. These items, where they point to and how, should be entries in the database or (better) the settings file that should have been there from the start. I should not have to edit the source code to link to my own YIM and ICQ images to improve load times, for example.
To be clear: BBCode, the postbit, menubar, and IM listings should be completely customizable, along with any similar lists - those are just the ones that strike me at the moment.
3: Use display hooks or rings to allow modifications to attach themselves to places without modifying the theme. A good example of this would probably be Drupal's block system, but ideally would have stricter definitions - here is a footer, here is a header, etc. and so on.
4: Pull theme options out of the theme. Especially things that don't have anything to do with the theme, like whether or not sent pms get saved by default, but even if not - if a theme needs a new option, it should be able to make one and give it a name appropriately.