We already have a shortcuts "feature", in a sense. Why not have a "Shortcuts" option in the main menu that takes the user to a list of shortcuts. These could be links to other menus, links to folders, or what not. Everything under "Shortcuts" is essentially a custom menu (mostly constructed by use of shortcut files, and possible folders of shortcut files to represent nested menus) but no customization outside of that?
Exactly. How can this simple feature of putting the shortcuts.link (and it alone!) to the main menu cause any "support nightmares" whatsoever? The feature HAS already been there, but it's less accesible.
There are two simple things to be done - adding the Shortcuts list to the main menu and making each shortcut run the selected option straight away (not directing to the file location, which forces the user to double click).
I understand the objections to the ability of removing main menu items (although I can't imagine how the option of changing their order would cause any troubles), but this has nothing to do with menu customization...
To the powers that be

- please consider this.
Rockbox is awesome as it is and this is one of the last things I can come up with as for the improvement of the GUI. Last but not least.