What I'd prefer is to have iTunes, Mac App Store, iOS App Store (split off from iTunes), iBooks etc all NOT BE APPS AT ALL. I'd prefer them to be seamlessly integrated into the system, maybe just menubar icons or widgets, always on call but never there till you call for them. Maybe a single "iTunes" icon in the menubar, which when clicked on offers a list of possible stores or your own library.

This would still be fully compatible with the older versions and the Windows version since it all pulls content from the same source, it would just be a more integrated way of presenting the info for Mac users.