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A lot of people who use multisite as membership sites or as a point for professional services probably go through changing the header, changing the footer, taking out menu options by user level. What would be ah-maaa-zing though is if there were an option to have your own custom user admin pages totally outside the wordpress panel.
OR, perhaps a slightly easier option, some sort of admin theming plugin that allows for some highly customizable CSS and admin template options. You can kind of get there by patching different plugins together now, but if there were a single one that did it all would be great.