I've heard that adding connecting passengers is a feature in development so I don't know how far along the concept is (i.e., whether it is still in the conceptual phases or whether there is already a plan of how to do so). However, I had an idea that I thought I'd share just in case it has not yet been worked out.
For simplicity, how about a 1-stop same-aircraft connection system? For instance, let's say you are an airline based at ORD and you have an aircraft that flies ORD-LAX-ORD and then it flies ORD-JFK-ORD. Currently, when the aircraft departs from LAX, it would only be carrying passengers who want to go to ORD. However, there is a pool of passengers at LAX who would also like to go to JFK but they will not be aboard the flight.
My solution would be for the program to perform a daily calculation for each airport. Have it look for any available 1-stop connections via the same scheduled airplane. Should there be any 1-stops available, assign those flights the "tech stop penalty". The remaining seats would be filled with however many connecting pasengers that airline won the right to fly (if any).
For example, let's say that demand for LAX to JFK is 500 passengers every day, 400 non-stop seats available & 600 1-stop seats available. But the 1-stop airlines fill 400 of their 600 available seats with passengers heading to their primary destination - leaving 200 seats available. The program then calculates how to distribute those 500 passengers across the 600 available seats.
The 1-stop airlines would get the technical stop penalty applied to them. They would then compete amongst each other and amongst the non-stop carriers based on the usual factors such as flight length (which, of course, is likely longer and further penalizes them), aircraft type, seat type, company image, etc.
Let's say there are 3 airlines that fly 1-stop through their hub from LAX to JFK - one at ORD, one at SEA, and one at IAD. The airline based at ORD would have a geographical advantage as the flight time would potentially be shorter - possibly giving them a larger share of the connecting passengers. The airline in SEA would be at a geographical disadvantage but they could make up for it in part by flying a larger aircraft, having a higher company image, etc.
This would also encourage more realistic route planning. I know many of my routes will tend to be back & forth in the same direction instead of following a north-south or east-west flow. For instance, an airline based in DFW might have an aircraft scheduled to fly DFW-PHX-DFW and then DFW-DEN-DFW. Instead, the connecting passengers feature would be more likely to encourage a routing such as DFW-PHX-DFW followed by DFW-ATL-DFW because there is a better chance the airline would be competitive for passengers going from PHX to ATL. PHX-DFW-DEN is about 778nm off of the great circle distance between PHX-DEN but PHX-DFW-ATL is only about 11nm off from the great circle distance between PHX-ATL.
Another beauty of this system is that it would make for viable connection hub airports. You could, for instance, build major operations in STL, DUS, PTY, etc. by scheduling efficient North-South and/or East-West routings and competing for connecting passengers.
Any thoughts on this kind of a system? I know it's not completely realistic since real-life passengers do connect on different aircraft and sometimes need more than one connection. But I think this would be a good start.