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Total fuel burn on an ultra long sector is higher than it would be for the same sector divided into two, given the same payload.
Payload for ultra long sectors is dismal. Basically most of the people, and all of the freight, are offloaded and replaced by fuel.
The gain, for all of this pain, is quite minimal. For a 9000 nm sector, total flight time is about half an hour less without stopping. Total trip time is about 2 hours less. Passenger loading would be so low (and the costs so high) that passengers (the few that you can actually carry) would need to be paying a very hefty premium. Most likely you're looking at purely business class, but you may not actually be able to afford the weight of the sort of seating that these passengers are used to. Upshot is that they'll get to pay more, but likely get less.
Just playing with some 380 numbers. For a 9000 nm sector (but using standard atmosphere temperature, and nil wind, plus assuming you get every altitude that you want, when you want it). Fuel burn would be 236 tonnes (which, plus reserve, is full tanks); flight time 19:15. Available payload? No freight, and about 200 passengers. With the same (obviously non viable payload), and two sectors, fuel burn is about 216 tonnes.
But, again divided into two sectors, and this time with a decent reserve of 18 tonnes, and maximum possible payload (i.e. max zero fuel weight), total burn is 240 tonnes, flight time 19:45, and you've carried maximum possible people and freight. Economics are dramatically different. ...
Another point...at intermediate landings, problem passengers are often removed. There are some people I'd rather not be stuck with....