Costs
You are taking on a broad task here as there are so many diferent ways to obtain a conclusion. Freight v Passenger carrying a/c are achieved very diferently. Many of the pax carriers work it out on seat cost which is the ASK (actual seat cost per kilometer) therefore the ticket price must aquate accordinly. Easy is reputed to be 4.5 - 5.0 pence per Kilometer and BA at the start of this year was about 13.0 - LGW / 15.0 - LHR. Some of the cargo airlines aquate it at minimum cost per kilo.
I was always told that much of it is inaccurate as like with cars many a/c do not perform to the manufacturers specification i.e. a/c is not as fuel efficient as expected therefore more expensive because it needs more fuel and may not uplift enough.
The aircraft performance can be costed on max take off weight, therefore how much can they carry, how much fuel do they burn in flight. How is the a/c performance effected by weather etc
Finally much of the equation is surrounded by mystery as many of the airlines only have the bottom line figure. Today they can only speculate on just how much business they will sell in two months time or how much money they will get for todays flying programme.