Transfers might work in Europe and Asia with a large network where people are accustomed to such things, but this isn't Europe or Asia. Europe and Asia have people willing to do things for transit because cars and gas are much more relatively expensive to them than in Canada, even with the gas prices we have recently. It's not a car culture there as much, in a nutshell.Transfers aren't unusual in the better used railway networks. Most passengers in Spain/France/Germany making 500km+ trips would be transferring. Cross platform timed transfer points makes these extremely smooth; far smoother flying from London to Ottawa would be.
Fare integration is wholly political. There no technical reason why a single entity couldn't sell a combined VIA/GO/... trip ticket. Many times when people fly they don't even know who's operating the aircraft, only who they bought the ticket from; selling tickets on another companies flight is common.
The majority of North American's have been turned off of trains because of poor service, and you are going to have to do everything to ensure it is a smooth ride that is nicer and cheaper than taking the car. A transfer at Union between two trains from London to Ottawa would kill the service here, even if it didn't elsewhere.