I agree that it's not much of a problem, unless you have a tight connection. One option would be to put everyone with connections in the front quarter of the plane (not first class, just the front of economy), but that would just annoy people who are fortunate enough to have direct flights. Fortunately most flyers know this and choose a seat near the front if they have a tight connection, even if they have to pay more. AC even advertises the fact that you can buy seats near the front if you need to deplane faster...not sure if other airlines do. Perhaps it should come up as a warning message when you book flights with a short connection.