But that's exactly the issue - it's part of a bigger problem overall.
All transit agencies in the GTA face similar funding issues, so my proposal isn't for Metrolinx to take over as a supramunicipal agency, but actually upload the responsibility of transit off the municipalities and onto the province.
Cities would pay some sort of taxes to Metrolinx for the management of transit, but the TTC, YRT, etc would remain as operating brands. Sort of how GO Transit is a part of Metrolinx.
Administration, control, etc can be centralized and savings could be found there - but having them all reporting to the same big daddy would make any integration project far easier.
And I strongly disagree the TTC is unique and cannot be handled by a regional agency - ever heard of Transport for London, or Vancouver's regional agency?