Dear James,
it is good to hear that Energy Plus has no limitations when it comes to the number of zones and I have to admit that I am looking forward to switching to Energy Plus in near future.
Since I do Energy modeling for living I can tell you for sure that sometime it is hard to escape a large number of zones. Take a look at one of my LEED projects that I did in the past http://www.designboom.com/weblog/cat/9/view/5818/ten-arquitectos-clinton-park-new-york.html . Please pay attention that residential part of the building on the perimeter has only two type of zones, bedrooms and living rooms, and they are all bundled up (per each floor) together when ever they have the same orientation (for
example, all bedrooms on the 22nd floor that are on the south side are one 22-BR-S zone ) plus there is a number of different HVAC systems serving different type of zones with different schedules in amenities on lower floors.
Not every job is like this, but in average I see between 50 and 100 zones per project easily.
Sincerely,
Vladimir.