If road tolls are implemented, I think they should be in the following fashion:
1) 7:30-9:30am, and 4-6pm on weekdays. Those are the times that the highway system is most congested, so that should be when there is a price attached to using them.
2) The system should be ETR, and set up so that it is fare by distance. This would act as a defacto charge on 905 residents, because they would be paying the most, on average.
3) It should only be set up on the Gardiner and the DVP to begin with. A 'border' system like London would be too expensive to implement right of the bat. If nothing else, direct some of the toll money to pay for helping to expand the system.
4) I think all auto-billing should be done using Presto. I know this may sound a bit weird to begin with, but hear me out: Presto's database already has the name, address, and billing info of thousands of people in the GTA. All they would need to do is add a field for vehicle type and license plate. This way the billing for using the tolls would come from the same purse as from using transit. For those who really don't want a Presto card, the bill would be send to the address listed on their license plate. Presto would just be a lot more convenient, because people could use the auto-load feature. And even if they were drivers, having a Presto card may tempt them to take transit every now and then. Presto would become the one-stop shop for all transportation payments in the GTA.
5) The system should be designed in consultation with the Province so that it can be expanded into a region-wide Metrolinx-run system. We don't need a white elephant toll system, where the rest of the GTA is using 1 system and Toronto is using another.