But the name of the line is Milton. ALL trains go to Milton. ALL trains start at Milton. Cooksville isn't a line. It's a stop. It's no more important than Erindale or Streetsville or Meadowvale or Milton. Does every station need its own schedule? Of course not, that'd be insane. The only one that's not like the others is Square One, due to it not being on the Milton train line.
I don't really see anything "confusing" about how the schedules are now. But maybe it's because I've been riding the GO for so long.
GO already has the QuickTables for all GO train stations. If they expand on those, that's fine. But there's no reason to get rid of the traditional GO schedules. Cooksville and Square One are not their own line. They always have and always will be part of the Milton line service.