I agree, Zones and Zone Switch have a great deal of potential, they're already probably way above what any other comparable media software would have.
It's already been identified above that Zones are in fact structured and they fall into a hierarchy - physical locations (which can be rooms, or PCs) and sets of audio settings within the location.
I think Zone Linking should also be structured so that you can link together any number of "leaf level" zones in any combination and multiple times. These "Zones" should be exposed as destinations to play to along with the original zones. In other words, we actually have 3 different levels in this hierachy, all called Zones as it stands at the moment! Taking mojave's example structure and expanding on it:
Living Room
- Stereo
- 5.1 Movies
- 5.1 Music
Kitchen
Deck
Bedroom 1
Bedroom 2
Bathroom
Downstairs = Living Room/Stereo + Kitchen
Upstairs = Bedroom 1 + Bedroom 2 + Bathroom
Bedrooms = Bedroom 1 + Bedroom 2
Whole House = Living Room/Stereo + Kitchen + Bedroom 1 + Bedroom 2 + Bathroom
In the Playing Now list, you would see the following as destinations:
Living Room/Stereo
Living Room/5.1 Movies
Living Room/5.1 Music
Kitchen/2-channel
Deck/2-channel
Bedroom 1/2-channel
Bedroom 2/2-channel
Bathroom/2-channel
Downstairs
Upstairs
Bedrooms
Whole House
If you want to add or remove a zone from a "grouped zone" while playing, it creates a temporary copy of the grouped zone that you can either save permanently under a new name or replace the original zone with. So the zone linking function as we know it would no longer exist and would be replaced with a Create and Edit Group facility.
Naming conventions for these three levels? Well...
1. Zone Group
2. Zone
3. Audio Settings
or
1. Zone
2. Location
3. Output
...
However, I can imagine that sync delay between these would be a pain to sort out...