the big issue with Hamilton Centre is the tunnel, and of course CP which hates dealing with Metrolinx.
The tunnel is designed for double tracks, and indeed was even double tracked in the past from my understanding, but does not fit double-stacked containers through it in a 2-track configuration from my understanding.. so CP doesn't let metrolinx build their own dedicated track through it and limits their operating windows to the morning and afternoon rush hours.
If Metrolinx had the money they could likely excavate the tunnel down to allow double-stack containers to fit in a 2-track condition and build a dedicated track from Bayview Junction, if CP doesn't just make them completely rebuild the entire tunnel. That would just be... expensive. Running the equivalent of 15 minute service through Bayview Junction would also likely necessitate a flyover there.
I agree that I hope we see it at some point, but likely not any time soon. The priority right now is clearly improving services on the CN line east towards Niagara.
Edit an old image of when the Hunter Street Tunnel first opened in it's original 2-track configuration: