I voiced my love for f.lux in a blog post here and on our podcast episode where we discussed iOS 9.3 beta. I preferred f.lux because of its ability to go further into the orange tint than NightShift which, to my eyes, was still too blue-yellow to really make a big difference.
I updated to iOS 9.3 today to find out that f.lux still works but for some reason it is not as orange as I remember it to be. So I took out my dSLR, locked the white balance to sun light (5000K), and do an exposition lock so all three pictures are captured the same way.
As you can see, my brain was not playing a trick on my eyes. NightShift is much more orange than f.lux! Just to be double sure, I reloaded the Xcode project on my iPhone and it is still the same.
So Apple apparently did something to the underlying API and it seem to have broken f.lux. Perhaps a default value is now different from what it was in 9.2 and the 9.3 betas. Anyways, f.lux is now out of my iPhone as NightShift is now the best of the two solution!