Several actually. The most obvious and substantial being the new A9 processor which is reportedly about 40% faster than the A8 in the older model. Also, the camera is a high resolution, now at 12MP vs. 8MP. Next we have the inclusion of 3d Touch which is a whole new screen technology allowing the screen to react to 'force' or how hard you push against it. There's some other more minor things such as slight differences in battery and also a new color available 'Rose Gold' only on the 6S and 6S Plus. Of course the iPhone 6S also comes with OS 9 out of the box, but the holder iPhone 6 can be upgraded to this.