As I promised earlier, I made a couple maps of a couple different fare zone configurations for the GTHA.
One of the things I tried to avoid is zones becoming 1 large ring around the entire region. So I used different shades of the same colour to illustrate the rings, but they themselves are separate fare zones.
The first option is a simplified fare zone structure with 4 rings as well as rural zones. The lines don't exactly follow municipal boundaries, because it's primarily meant for rapid transit, which should be under the control of Metrolinx.
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The second option is one with many more fare zones broken down. This would be a more ideal structure for rapid transit, because you could have a base fare and then an added fare for each subsequent zone travelled. $2 base fare for local transit, $2.50 for rapid transit (BRT, LRT, subway), and $3.00 for express transit (GO REX, GO Trains, GO Bus, Express Buses), followed by an additional $1.00 per zone would give a pretty fair fare structure.
Unfortunately though, it could be very confusing for some riders at first, although hopefully with Presto and tap on/off it should sort itself out automatically.
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What I'm thinking for how it works is local transit does not travel through more than 2 fare zones. As a result, a tap on on a local bus charges you the fare for 2 zones. If you stay within the same zone, tap off when getting off and it will refund you the extra $1. I find that the refund model would be much better than asking for money twice.
For rapid and express transit, what would happen is you would be charged for how many ever zones that route passes through. If you exit before the entering the total amount of zones, you tap off and you get refunded the difference. For example, if a rider is riding the Yonge Subway, it passes through 3 zones (you can ride it around and pass through 5, but that wouldn't make any sense to actually do). When tapping on at say King, you would be charged $4.50. If you tapped off at Eglinton, you would be refunded $2.00. This $2 gives an incentive to tap off, and it also reduces fare evasion.