nice. thats awesome. as my map has pre-placed cities and improvements it wouldnt do a whole lot but thats great.
If your map has preplaced cities and improvements, that makes it a bit simpler to retrict the number of cities with air trade activated.
If you have not used up the 32 maximum combined strategic and luxury resources, you can create a special resource, call it Airport Resource, and require that to be present within the city radius for an Airport to be built. The resource may have no other benefit (I might give it one gold for airport tax revenue), it only allows you to have an airport in that city. Then decide what cities should have the airport allowed, and place the resource there. If you have used up the 32 strategic and luxury resources allowed, then either use one of the available resources, say aluminum, and require that to be within the city limits, or go to a combination of two resources needed within the city limits. That should quite effectively limit the number of cities with air trade activated.
You can do the same thing with harbors to limit the number of cities with water trade, although that would depend on the type of map that you are using. On a Pangeae map, that probably would not be an issue, but on a continent or archipelago map, you might want to allow harbors as needed, without a resource required.
Lastly, with respect to air trade, you could also create several Small Wonders, available with either Flight or maybe Advanced Flight, and have only them allow air trade to take place. Call them say, O'Hare, LAX, Heathrow, Dulles, Kennedy, Midway, Mitchell, etc., and then you can place them where desired or have the option of building them where you discover that you need them.
I hope that this is some assistance to you.