I think one of the big issues for ML is getting rid of the grade crossings. While it may not be a big issue on the outer areas of the service ie on the way to Barrie or Kitchener, for the RER {or whatever the hell they are calling it now} it will become a necessity.
Right now, the increases in GO service are welcomed by the public but as service levels increase exponentially, the push back from those same citizens will become
very vocal. It's one thing to have a train going by every 15 minutes but when service is increased to trains going by every 6 or 7 minutes in rush hour and every 10 minutes all day, people will start to get pissed off. That will mean that a train will be crossing that street every 3 or 4 minutes bringing traffic to a near perpetual standstill and, having to listen to those VERY loud train horns every time it goes by. It would be enough to drive anyone nuts and will become a real issue as residents will be infuriated by it and I can't say I would blame them.