The idea of fare zones is one that I have always supported and it looks like this is the one that will be implemented and that's nothing but good news.
I think this map has too many different zones as they should be done on a regional basis. Halton should be one zone as should Peel and Toronto. There can certainly be exceptions where there is a clear distinction between urban & rural areas or the regional government boundaries are huge like Caledon in Peel, northern York, and Durham. Still the idea is sound. Not only does this make sense from a operational point of view but also a taxation one. Some taxes are levied or transferred over to regional levels and so they are easier to administer on a regional basis but also it makes sense for the individual rider. A person may not know "technically" whether they are crossing into another city but certainly know when they are crossing into a different county/region. This is what York Region did well. You don't have to worry about crossing some silly artificial boundary between RH & Vaughn and you shouldn't have to between Oakville & Burlington, Brampton & Miss or within the City of Toronto.
There is one BIG caveat however.............the zone fares must apply to ALL transportation options including GO. Only one person knows the best way for the rider to get from A to B and it's not City Hall, Metrolinx, or a policy wonk but rather the rider themselves. They know what's best for them and whether it's commuter rail, RER, subway, bus, LRT, streetcar, horse & buggy, or all of the above is irrelevant, going from A to B should be the same price no matter how you get there.