Notice how I mentioned people commuting to anywhere south of King. Anywhere else will be slower. Currently, the trip between Kennedy and downtown is 19 minutes. When you throw in 2+ more stations along the line, then the time will probably increase to around 25 minutes of travel time. Compare this to the subway, which currently, from Kennedy, is 36-38 minutes depending on construction and the time required to transfer at Bloor Yonge.
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Now that seems fine, but note: this is only for Union Station. What happens when you need to go anywhere other than Union? What about Queens Park for Uni Students, or the Eaton Centre for shoppers?
Queens Park by Subway: 35 minutes
Queen's Park by GO and Subway: 40-45 minutes depending on transfers (Google maps states that there is no transfer time between GO and the TTC, but we all know that it's at least 5-10 minutes with the 3-5 minutes to get off the train and get to the concourse, the 2-4 minute walk, and the 1-3 minute wait for a train.
Now: frequency times -- Since RER stations will have frequencies of up to 15 minutes (compared to the subway's 5 during off-peak hours), we'll assume people will have to wait twice to three times as long for a train. With this, you can add 5 minutes to the journey, and the subway journeys will get a 2.5-minute addition. At this point, RER is looking much less attractive.
I'm not against RER, I really want it to succeed, but people are vastly overstating its benefits. The subway gives you the ability to get to more destinations than RER (depending on how many stations are built). The vast majority of people will still want to take the subway because their destination does not lie within a kilometer of Union Station. People what will take is convenient for them. As a result, I believe it's important to advocate for both excellent RER and excellent subway service.