I have a solution to this issue (that I and others have previously suggested), but it's a very complex one, requiring a complete overhaul of the trade system. Trade routes as they are are really not of great importance. You do not really have any influence over trade routes. By making a system whereby trade routes, although automated, are visible and customisable, and have varying outputs, depending on the expediency of the route taken, you would allow for a far more complex trade system. Add to this the importance of rivers, and you now have a use for rivers as very effective trade routes, and therefore very effective economic tools in the game.