Using a separate admin theme would allow you to avoid some changes, but you'd have to look through and figure out which are changes just for styling purposes, which you could avoid, and which are functional changes which you'd probably have to integrate.
As for S, there aren't any current plans to make modifying the admin easier. It's possible, and perhaps easier, with an S module, as the more modular nature of the system makes overriding any view, including an admin one, accessbile to any module. However, the same idea of the "real" admin changing and updates needing to be integrated would probably remain.
I'd be interested to know what kinds of changes you're making to the admin. My preference would be to make things work so that customizations can be applied by more targeted modules or perhaps preferences, rather than having people have to resort to direct changes to the admin views.