My question is what determines these routes if not weather?
Just a few thoughts:
Attempt to reduce Navigation charges (ATC charge for their services, some charge much more than others).
Aircraft equipment/temporary minor defects might restrict the route of flight (perhaps a minor defect means the aircraft has to stay within a relatively short distance of en-route airfields).
Maybe a decision has been made not to a route the flight through an area of possibly severe turbulence/inclement enroute weather.
Might be something as simple as having plugged in all the variables Company A's computer reckons going north is cheapest/best, whereas company B's computer has come to a different conclusion....