Currently there is nothing to negotiate in terms of interlining agreements since there is no monetary agreements involved.
It would be awesome if it could work the following way:
When specifying an interlining agreement you also specify an "administration fee" which is what each transferring passenger has to pay for the connection on top of the ticket prices.
This can be set between 0 - 30 AS$ per passenger which ensures backwards compatibility (All current agreements are treated as if they have 0 AS$ fee).
Of course setting this high will lower the rating just like having to long connection times will.
This also enables the fun part! When negotiating an IL agreement the two involved airlines have to agree on how to split this fee, if the agreement works very much in favor of one airline they can demand 100% of the Interlining fee to make up for their troubles. For example a situation where one airline is operating as a feeder with almost no profit margins, and the other is able to charge high profit margins from long haul flights off the same passenger.
In the agreement you are also able to specify what company will pay for / provide the flight planning staff. Today company A and B both pay for say 5 staff each, I suggest they get to divide the 10 staff required as they see fit between them.
So you could even offer and agreement where you agree to pay for all the flight planning staff but also get 100% of the fee. The other airline risks nothing but also has nothing to gain if it turns out to be such a successful agreement you even can run a small profit of all the IL fees charged!
Another upside of this is that you can see what IL agreements are working well since a more detailed summary is required in the IL overview specifying how many transferring passengers you have and what you gain from fees in each agreement.
I believe this would greatly increase immersion of actually running an airline that has to negotiate real agreements with direct monetary impacts.