It could be an idea to setup the ability to make plugins that could work just on mobile. Or have plugin developers include something like "mobile" folder in their plugin, and needed files e.g: mobile.php, views.php, images, etc.
This way, the main version, and the mobile version are different looking, but are webbed with the same data, and plugins could show up fine on mobile version too.
Also, same for the themes. The system contents of that theme should include mobile version too, that could be displayed when a user is accessing via a mobile device. So, I guess my philosophy is that it needs to mainly be concentrated on statics and themes, even though data plays a big part, you can just snag that from other site contents, and the site DB.