The biggest challenge with building transit in North America is that transit is used as a political tool, rather than as a way to move people around. Elsewhere in the world these debates aren't anywhere near as politically charged, and building a transit line is little more controversial than announcing a road repair program.
Metrolinx was supposed to de-politicize the whole thing, but with power in the Government of Ontario being as centralized and secretive as it is, Metrolinx was quickly co-opted as a PR mouthpiece of the Government of Ontario, rather than doing anything genuinely useful to get transit built in the GTHA, that couldn't have been accomplished without its existence.
I think de-centralizing Metrolinx might be a wise move. That means removing the Government of Ontario from the business of building transit, and turning Metrolinx into an independent non-profit corporation with taxation authority. It would be accountable to GTHA municipalities through its board of directors. That would put an end to the days of Metrolinx being PR fodder for the provincial government of the day. And with individual municipalities and governments being unable to control Metrolinx's agenda, the agency would be able to build transit, despite cries from its constituent municipalities or the provincial government.
But honestly, I don't even know that would work. There might not be a way to de-politicize this whole process. The political nature of this might just come down to cultural reasons. With North Americans being as individualistic as they are, I get the sense that people are more concerned with how transit benefits themselves personally, than with whether or not it benefits the city or region as a whole. If that's the case, then building transit will always be tremendously difficult; there are always winners and losers in this game of transit expansion.