First of all I don't think your first point really applies because this project is already getting delayed by another 3 years - I have a hard time believing it won't be delayed further. Yes it's a larger plan than the previous one, but further behind. This is why a phased approach can be helpful.
There's no reason Ford couldn't have fast tracked the existing plan, designed in conjunction with local stakeholders, and started immediately on the DRL North to Don Mills.
The GO transfer is good in theory, though I do question how often it'll be used.
The last three bolded points I don't agree with because the government isn't operating with any consistency. If anything, suburban residents have been told above ground transit is unacceptable, and are currently getting projects that support that position.
New trains - new is nice, but they don't seem a fit for this project, where capacity is crucial.
And finally, we shouldn't need to cut corners to force regional agencies to integrate fares.
Innovation is a great thing, but we're not seeing that here. If the 'innovation' undercuts the primary purpose of the project you have a problem.