I don't think they'll allow it. Apple seems to be far too proud of their UIs to allow any theming. As far as I know, OS X doesn't allow theming either.
+ Maintaining compatibility for themes would be a nightmare. There are many themes in Cydia that replace application icons so that they fit the theme. It would be nearly impossible for developers to make alternative icons for every single application in the app stores, so Apple wouldn't want to implement 3rd party themes. I could see Apple adding a couple alternative skins that they develop and include with the phone, and mandate the developers to include icons that match these limited options. Even that is highly unlikely imo.
+ Maintaining compatibility for themes would be a nightmare. There are many themes in Cydia that replace application icons so that they fit the theme. It would be nearly impossible for developers to make alternative icons for every single application in the app stores, so Apple wouldn't want to implement 3rd party themes. I could see Apple adding a couple alternative skins that they develop and include with the phone, and mandate the developers to include icons that match these limited options. Even that is highly unlikely imo.