Is there a way to block the citizens? To prevent them to walk through e.g. orchards, pastures, walls & fences, etc? I would like them to take the paths and roads. Also, why do they take a short cut over a mountain when there is a road around the mountain/hill? You can't lay a road on the route they take, but they still keep taking this shorter route.
I think the computer calculates the shortest time it takes from the place they were to the place they are going to. I think there are some mods, that makes the Bannis walk faster on roads, I haven't tried one of those and I don't think there are any on this page but maybe on banishedinfo.com.
For some special space, you don't want any Banni to take a shortcut over, it's always this: http://worldofbanished.com/index.php?action=downloads;sa=view;down=294 It´s just an empty square but it prevents the Banni to pass. I think you can't use it everywhere to keep them on the road, but on some irritating locations, it might help.
Otherwise, the only help I can give is to wait a bit to build roads and build them where people walk. I know it's not always possible and I guess you have to live with some shortcuts.