Personally, I think that services like the Northlander, Toronto-Sarnia, and in the future Toronto-Kingston & Ottawa-Kingston (once the HFR corridor is finished) should be run by Metrolinx under a separate, Province-wide rail banner (i.e. not GO, maybe called ONrail or something). That would let VIA concentrate on the QC-Windsor corridor, and those communities wouldn't be beholden to the Feds to provide rail service.
It would also make things easier to be operating multiple lines under the same configuration, since you get consistency in terms of vehicles, maintenance, employees, etc.