In Japan they have trains that are 6 car express trains, 2 cars have reserved seating and the rest have regular seats. The objective is to allow transit to be more competitive. Why have overlapping services?
Because overlapping services can have different stopping patterns and thus different speeds. Japanese mainlines have tons of different stopping patterns too. Even the Tokaido Shinkansen has three stopping patterns: Kodama (local), Hikari (express) and Nozomi (super express). And the Nozomi also has different ticket conditions, so certain passes are not accepted whereas they may be on Kodama or Hikari trains.
Sure, GO could theoretically be set up to enable different types of tickets (reserved/unreserved seats, first/second class, etc), but there's not really much point in doing so, since VIA already offers the alternatives that GO doesn't, and there is plenty of other difference between VIA and GO offerings to justify overlapping along a corridor. Namely that VIA trains make far fewer stops, require tickets booked for a specific train (because they're lower-capacity trains than GO) and continue outside of GO's service area.
GO's planned all-day Regional Express services to destinations such as Kitchener, Niagara Falls, Hamilton and Barrie certainly have the potential to infringe on VIA's market, but I think that there is plenty of room for VIA to move upmarket to avoid redundancy. For example, VIA trains to Kitchener currently take about the same time as GO express trains, but ticket prices are much higher. If VIA were able to drop some intermediate stops and offer shorter travel times than GO, their product could be positioned as a premium-express alternative to GO's fairly basic Regional Express services.
If I live in Hamilton and need to go to Oshawa for a meeting, driving THROUGH Toronto is such a pain, but if the train could get me there faster and ran at all times during the day it would make it more attractive. Currently it takes double the amount of time to take transit than to drive, if you could make this comparable to driving, more people would take transit.
Yes, and once GO starts operating all-day express trains from Toronto to Hamilton, it won't take as long to cross the region on transit. Ideally the Hamilton express would continue through to Oshawa, but that may be somewhat limited by the discrepancy in track capacity west and east of Union.
Lakeshore West will have 4 tracks, while Lakeshore East will only have 2.
Kitchener will have 4 tracks while Stouffville will only have 2.
Barrie will have 2 tracks, while Richmond Hill will only have 1.