I think this whole issue could be achieved by putting an "Expression Manager" entry into the Options menu.
Using this manager, we could add and store expressions. These could then be accessed when using features which use advanced expressions or calculation fields. For example:
1. Rename file from properties
2. Edit View Scheme --> Add --> Advanced Expression
3. Calculated data in the Custom Tag creation menu
In the manager, we could define rules for doing specific things (like Otto updating filenames or paths). We wouldn't have to end up with messy folders like iTunes, as we could specify exactly when and what we want it to do and which files will be affected.
It is fully customisable at the options menu level, but will be much simpler to use in the areas mentioned above (can simply select a saved expression rather than typing it out each time)
As far as renaming files go, we could set up renaming categories and be able to pick which template we'd like to use for each group of files. Once this is selected, MC automatically updates the filename as relevant fields are changed.
If we never define a rename category, MC does nothing and we get no mess.
Any thoughts?