Isn't the subway network profitable? It's why I don't think there's an issue if Metrolinx takes over. They'll reinvest further. The city will have to appropriately subsidize feeder bus service.
Also, I think fare-by-distance or zoned fares will only happen when the subway network and the feeder network are separated. The TTC seems to have no interest in it.
And if one think uploading equate to a process free from political interference, all they need to acquaint themselves with is why the province chose to fund Spadina extension, or build a station at Kirby.
AoD
Whichever level of politician controls it there will be political interference. Just look at the fantasy maps various Mayor's have produced as platform gimmicks. Every swing voter somehow had a a pretend station near their house. Scarborough, Finch, Don Mill, DRL, Jane. Mayor's did not focus on the feasible or the most needed but which ones scores votes in certain areas of Toronto.
Provincial will somewhat do the same. The DRL has turned from a Relief Line into a Downtown focused subway since there are lots of NDP/Liberal swing votes in the downtown ridings. PC's will focus on the outer-416 and the inner-905 since these will be swing PC/Liberal's.
So the question is how to make sure that the tax dollars are spent that would best each persons needs and is transparent (so politicians would have a hard time interfering). Yes, there would be fudge-able numbers in any formula but here is my attempt at a solution.
What I would like to see is a property tax charge for transit (just like we have for schools) in the GTA. To cover both capex and opex of the transit system. 1/4 goes to GTA regional transit (e.g. GO), 1/4 goes to very local transit (local bus service or streetcars), 1/4 goes to intermediate transit needs (subway, BRT, LRT) and 1/4 goes to mega-projects (RER). Take the average throughout the GTA right now that we pay through our property taxes and apply it across the region. And the Province will contribute 1/2 mega, 1/4 GTA and 1/4 intermediate (capex and opex).
Then the transit agency (whomever it is) would need to report on what services they have provided to each resident specifically (including an annual report card plus mandatory community feedback on priorities). For local transit it would be more of a subsidy to cover operating costs. But for regional transit it would be more capital growth.
This would mean that users in dense neighbourhoods may have surplus balances which would allow more frequent bus service or a LRT service being built to serve the neighbourhood. And in less dense areas that currently do not have bus service it would force the City to figure out the best way to service the community (Uber?). It would also mean building a subway/BRT/LRT to neighbourhoods who are being undeserved right now (comparing dollars contributed to dollars used).
If you live beside a subway it could mean building a tertiary exit or building a relief line that you would use.
It would also mean commercial buildings also have the same formula. This will mean that money will be allocated to make sure employees can get to work & people can get to the retail stores (the transit needs are met not just for the residents but also the workers).
The downside…dense areas (i.e. the financial district, Liberty Village, etc) will get more and more transit while other areas will continue to see ½ hour service. But I would consider this an upside as well. It makes sure that the transit dollars are spent on the areas where there is density and where there are transit needs vs White Elephant projects. And lots of transit will drive more density creating growth nodes.
If a developer wants to bring a subway to their undeveloped area (e.g. VMC) they would have to agree to fund any deficiency (including a surety bond) until the development hits the desired limit.