With Windows 7, for those of us who wanted to organise our menus but had some apps that demanded menu folders or links to be there (arghhh) I used to hide the folder or link in Windows 7 - a bit rough and ready, but worked quite well.
Start8 does not seem to honour the hidden flag - so can it either do so, or even better allow menu items and folders to be hidden within a user's settings for Start8, allowing apps which demand the start menu items to be for all users to be managed only shown to those users who need them. This could allow you to hide all of the metro programs that have to be at the root of the start menu from users.
Maybe a right click on the item or folder and a "hide from user" option. Obviously would then need a way to unhide them as well, maybe through the main settings screen somewhere.