In reading the discussion regarding pak balancing here, specifically addressing DrSuperGood's well put post about the ease of building a network of any size, I've come up with ideas towards making planes more difficult to set up, reduce their superior flexibility and increase simulation depth. There are four main points of the concept.
1. Speed limits dependent on cruising altitude.
2. Introduction of waypoints/towers that determine the height/altitude a plane flies at.
3. Increased costs for planes climbing heights.
4. Change the routing of planes to only fly straight to the destination.
1. A plane is not allowed to fly 500mph 400m off the ground, for obvious reasons of safety, health, etc. But they are allowed to fly and capable of flying at those altitudes, usually approaching landing. So if there is a set of rules for various speeds at various altitudes, one can find a way of limiting the speeds aeroplanes travel at. E.g. while a propeller machine flying at 200km/h is allowed to sit at a comfortable 3 tiles altitude, a jet engined beast capable of running 900km/h is confined to 7 tiles or higher before being allowed to reach such speeds. Super sonic flight could only be allowed at max height over sea level.
3. When a plane increases its altitude, it consumes a lot of energy/fuel in doing so. This consumption differs strongly from cruising behavior. So if a plane changing its altitude costs a multiple of what its cruising cost is, players won't be tempted to add a height=16 marker after the runway, because it renders the plane unprofitable for fuel cost. Additionally, slowing a plane while climbing could factor into speed bonuses.
4. Currently every plane (and ship) knows exactly where it's headed and will always find its way. If we bring in the fact that a plane/ship orientates itself and find its way based on perfect knowledge of the map, that's fine with modern vehicles but fairly unrealistic when it comes to pre-computerized vehicles. Using markers to guide vehicles otherwise headed straight for their destination to avoid obstacles would/could complicate things and challenge players by either flying their planes over a mountain range or choosing a valley instead to conserve costs. Routing (which I recall being very resource-intensive for ships) could be simplified (same principle as building a way while holding ctrl) and a route via markers to a stop markers checked, rather than just to the next marker. This is to specifically to ensure that before landing the correct height above ground is chosen.
TL;DR: Planes now have to worry about height/altitude for fuel cost and allowed max speed, which they read from markers/waypoints. Also, planes need waypoints to orientate their heights at least for landing purposes.
Due to limitations of the simutrans graphics engine, any object higher than 6 tiles might not be drawn correctly, whether it is buildings or planes. So, until the planes are draw separately (maybe as a flying overlayer), those planes will always fly too low. (On the other simutrans scale of 1 tile one 1km, theose planes are not to low, since 1 tile is (in 64 size) 32 pixel across and planes flow between 6x and 12x that value.
That's a shame. The amount of changes would be vast and only benefit one relatively small area of the game.
Ok, I think my answer were too short: Currently planes travel at 4/max_spped when they are lower than 3 tiles (on approach or circling).
Currently, a plane will take the shortest route to its next destination. This would remain in place, the idea of the forced waypoints is to simplify a plane's routefinding capabilities, forcing the player to construct routes by checkpoints.
Is it possible to adapt the ctrl + drag construction path finding into vehicles? That direct routing should be fast and simple. They shouldn't check all tiles for candidates, but go straight to the waypoint tile and only read instructions from that tile.
In theory, ships could use the principle to reduce the "set destinations and forget about it" by requiring line of sight to lighthouses for changing direction, but that's probably not viable.
Planes currently only go in straight lines as you mentioned. However, as soon as this does not work any more, the expensive real pathfinder must kick in.