One suggestion I made was renaming the header/class files for Zune. If that's all that's needed to allow Zune and MUI to live alongside each other, then it's an acceptable compromise IMO.
Just implement zunemaster.library and install Zune custom classes in SYS:Classes/Zune. No need to mess with header files.
To explain, imagine if Application.mui is equivalent to Z_Application.mui. As long the compiler found the functions it needed in Z_Application.mui, then there needs to be no further changes, so it's really easy for applications to move to using Zune.
Actually no need to because MUI/Zune classes wont appear in BOOPSI class list.
Also remember that the compiled program will not keep a record of our name for the function, but merely where to find it and how to call it.
The problem is you have to recompile programs to use Zune this way. Existing 68k software would not be able to use Zune, neither would existing MorphOS software use Zune.
On Amiga 1200 on the other hand if Zune was used to replace MUI it indeed makes sense but of course Zune must be binary compatible.