I personally disagree with zones that are based on street/station boundaries as it will unfairly punish people on the boundaries. Someone going from Lawrence to Eglinton shouldn't get dinged more than anyone else travelling one stop on the system. Zones could be created, but based on where your trip originated from and number of stations or kms travelled. I also think the rates should reflect time of use and demand. I'm sure current technology exists to make this feasible, obviously it would have to be a completely electronic system, but I haven't thought about the implementation much or if it is something PRESTO could easily be converted to.
There's another thread on here about pricing congestion on the roads which I thought was a great read, and think a lot of the ideas could be applied to the subway system which itself seems to be a scarce resource (particularly certain segments) and capacity seems really hard to add.
I don't have problems with subway in the suburbs. There are plenty of major office clusters north of Eglinton. If someone from Richmond Hill Centre wants to use the subway to get to their job at Finch, then go ahead by all means. However if they want to use it to get to their job at the Financial District and not use the GO service (because it is currently more expensive), then I have a problem with that. The subway for long haul distances should be priced HIGHER than GO because of the all day frequent service and destination possibilities it provides you. It is a premium service, and its price should reflect that.