I don't think it was a weakness. His weakness was not being able to keep up with the pace without depleting the energy in his muscles. He probably could have ridden a long time had the pace been lower.
It's not a secret. It might feel like it if you don't know Norwegian though. 
If I understood the interview with his trainer on tv correctly, what makes him special is his combination of fast and low twitch musculature, and in my own opinion that he has had the same trainer since he was 14 and they have followed a long term plan of development.
According to his coach, Kristoff can burn fat instead of muscle in long races. That means his sprint is only marginally affected after a long race, while most of the others have a big problem getting a good sprint going. In theory he could ride 400km's and still have the same sprinting capability.
This also means he is less affected in a tour, since he is burning less muscles relative to the other sprinters.
So lets say Kristoff starts the tour with 1500w sprinting power, while Kittel starts with 2000. At the end of the Tour Kittel is down to 1600w while Kristoff is down to 1450w.
He is scheduled to keep improving, so it will be interesting.
As for Sagan and EBH, they probably have a different balance of fast/slow twitch muscles. Also they have not been coached by Stein Ørn since they were 14.
Ørn is also a trainer for the guys at Østerhus-Ridley, so it will be interesting to see how they develop in the future. 
According to Kristoff himself, he has not made any major leaps in performance, it's just that the few percent he improves each year meant that he at some point could keep up with the pace.
Sorry if I'm not making sense. This stuff is not something I know much about.