We know that Touch ID could be one of the reasons, and thanks to a recently discovered patent (via MacRumors), it has been revealed that perhaps Apple has plans for the physical button to turn it into a possible joystick-like device. As you can see in the image above, it shows the two states of the home button.
The left image is the home button in its regular state, and the other (which has been raised) is in joystick mode. The image of the springs also suggests that pressing down hard on the home button would release it into joystick mode. The patent filing also reveals Apple’s acknowledgement that gamers are hesitant to play games seriously on phones due to their lack of physical controls.
Not to mention onscreen controls tend to block some of the display, so hopefully with a physical joystick built into the phone, gamers will have more screen real estate to play with. It is also the answer for gamers who are unwilling to spend money on or carry around gaming accessories. However given that this is a patent, there is no guarantee that Apple will actually follow through and make this a reality, but it’s an interesting concept nonetheless.