I'm mostly familiar with trains in Germany and I know a comparison is unfair, but it seems like we're missing an entire part of a coherent transit system.

We have Via trains, that can loosely be compared to Inter-city trains. Long distance between cities and more expensive. We also have commuter trains like GO and Exo that serves a metro area and all the suburbs around. They are cheaper (subsidized), you can get a monthly pass, no seat reservation, and they are more frequent (than Via trains).

But we have nothing akin to regional rail. I'll just quote a definition from Wikipedia:

Regional rail usually provides rail services between towns and cities, rather than purely linking major population hubs in the way inter-city rail does. Regional rail operates outside major cities. Unlike Inter-city, it stops at most or all stations between cities. It provides a service between smaller communities along the line that are often byproducts of ribbon developments, and also connects with long-distance services at interchange stations located at junctions, terminals, or larger towns along the line. Alternative names are "local train" or "stopping train".

I understand the people complaining in the article, but as someone without a car, I also rolled up my eyes and thought 'but what did they expect from Via?' Exo and GO trains are specifically for commuting but they don't reach them. Relying on last minutes tickets from Via for commuting is, IMHO, a bit insane. They are missing a regional train. Right now our society expects them to drive their car (electric!) to Oshawa then use GO, if they want to commute by train.

We are missing regional trains in Québec too. It's equally stupid that someone can go from Montréal to the end of an Exo train line for $10 while the next city with Via would cost triple that, and with less departures. There's also two rail lines between Montréal and Sherbrooke. Both are used for freight, but no passenger trains. I'm still salty about this one because the little town where I grew up, on one of those lines, had passenger trains for more than a century before being cut by Paul Martin in the 90ies.

Beyond the recurring issues that you mentioned with the priorities and the lack of tracks, neither our provinces nor the federal government have any cohesive plan for transit. It's either by city and metro region, or Inter-city with Via or coach. Nothing in between. Even if we give priority to passenger trains, we're stuck with a ginormous car culture that says trains and buses are a waste of taxpayers money. I would really love to see more investment than just in Alto, even if it's still a good thing, but I'm afraid Via is going to stagnate for a while longer.