Why are Pages/Numbers/Keynote not free in the App Store on new iPhone 6s?
After taking it up with Apple Support, here is the answer:
The first user (AppleID) which activates a new iPhone gets those apps free. If the iPhone is reset to defaults and another user (AppleID) is used, which is what I did, then that user does not get them for free.

So the free option is a one time thing.