Interesting thing about the shift option. I've already limited my air trade routes to a 'Customs house' building which require the capital building, and a special building called 'Trade post' which require resources within it's radius (usually by coasts), and completely scrapped naval trade routes. My harbors only increase food on water tiles, and commercial docks only increase trade on water tiles now.
In addition I gave these buildings a 'Naval bombard defense' of 1, so that they are target-able by enemy naval bombardments, clearing trade routes in late game wars to speed up the game when blown up, or simply using the functionality as a trade blockade effect.
It is also AI compliant since they will also bombard your cities with navies and break your improvements.
I'm interested in finding out if also giving these buildings an 'Air' value of 1 will make them more likely to blow up when an air attack is successful against it's city.
Note for random maps:
Limiting the AI to build trade routes only through a building which requires a resource that spawns on coastal tiles, and is within it's city borders in order to speed up the game can be AI compliant with some tweaks. Since the appearance is gonna be random, to reduce the chances of the AI possibly never being able to connect other land masses you'll have to create a sea worker.
With a sea worker the AI will build a road across oceans to connect other land masses to all of it's trade, and make that a worker priority for what I've seen in my tests. This way even if the appearance ratio was not a very fair one for the current map they can still connect land masses, and so will the human player.
Another thing to keep in mind would be to give pillage to some naval units, so they can disconnect trade routes in war times.
Remember you'll need an editor such as Quintillus to achieve this.
I've done these changes and my turn times are much better. Usually 30 sec to 60 secs in a 180x180 late game map. Well that and I don't allow settling on Ice or deserts along with settlers being auto-produced till the colonization era in the industrial age to slow down the pace of trade route making via road making and city building. In the original game by late game the whole world is railroaded and cities on every corner. That also slows down the game when the world is over developed with too many cities and trade routes through roads, and quite frankly not very realistic if you compare it to real life.