Age old question
Did a fuel analysis for a year on same routes to cover all seasons in long haul. Higher CI compared to the bean counter's lower CI seemed to be most efficient use of fuel for time flown. Consistantly arrived with at least the same fuel remaining with much time saved. Knowing that, the proper CI should include additional factors such as fuel cost for that sector versus historical revenue stream for same sector. Obviously a freighter with higher revenue should fly closer to the minimum time/fuel available CI than a passenger flight. We are only talking long haul here; > 4 hours flight time.
I believe the sophistcated software does exist that could be employed every day for each sector to included pax/frt load, environmental factors and fixed costs. Could save a lot in the bean counter's salaries.