If the issue is that Armies/Merchants/Travellers could (in the real world) move long distances quickly by river, then could that not be simulated by making the routes of large rivers easier to move along? What I mean is, armies move further per turn on roads than across open country. Could this be applied to river courses? Essentially you'd put roads (invisible roads?) alongside the important rivers, allowing units to move along them quickly, simulating river transport.