As much as I like this...
I'd love to see more direct-to-downtown service -- but both CN and CP put a price on letting Metrolinx use their rail for passenger service, and may be reluctant to give guarantees.
From what I'm witnessing, and construction site photographing, I see far more infrastructure happening on the CN side of things -- my
earlier 2015 pictures and especially the Metrolinx-funded
Hamilton Junction expansion where I witnessed pile-driving on February 19th, 2016 for upcoming rail bridge footings there. That could tip the scales, if CN was willing to provide a schedule guarantee that CP was unable to accomodate. Freight companies are notoriously finicky about sharing with passengers but the negotiations with CN may possibly be going better.
Also observe that the Niagara area mayors are wanting to also
PULL people into their area by GO trains for work,
with their massive pre-emptive Niagara GO train investments and their recent success in getting a Welland Canal GO train priority-over-boats guarantee! These Nigara mayors are preemptively
paying 1/3rd of the cost of the upcoming Niagara commuter GO train service -- that potentially means counter-peak trains that makes a Hamilton stop. Toronto->Hamilton->Niagara in the morning, and Niagara->Hamilton->Toronto in the evening. 14 trains a day, 7 each way, and it's probably going to end up being service in both directions because of the Niagara-area municipal pay-ins.
My betting man bet if there was one: It's
West Harbour GO for counterpeak service. Trace the money and construction site activity, and it looks almost virtually certain West Harbour GO is going to be the first one to get counterpeak service. It's likely Hamilton Downtown will probably only get peak-direction service for now.
Bet your mortgage on it. Even if it's not the most appealing option for all Hamiltonians.