|Shortcut Choice by category or Location|
I would think that the user should have control over where in the menu shortcuts go.
To standardise this I suggest that Windows Installer define a set of categories (which the OS possibly also uses) and defines these.
So my MSI might be classed as a "TOOL" and perhaps have a subcategory which is standardised or defined in my MSI, either way it goes there by default. Other categories might be "MULTIMEDIA", "MULTIMEDIA_AUDIO"...
The user should be able to override the default location.
The problem now is that they go whereever and users move them, this is particularly bad with advertised shortcuts (which will stop working on update) but are good for none. A lot of users dislike MSI partially because of this.