Imaging Resource reports that a 12MP image sensor inside iSight cameras on the new iPhone 6S and 6S Plus feature two new technologies:
"The first of these is the decision to move the color filter that normally sits above the sensor directly onto top of the pixels, leaving less room for error. The second technology is the use of what Apple calls ‘Deep Trench Isolation’, which puts small dividers between the pixels to prevent light from bouncing around unnecessarily."
A Youtube video from today's Apple event shows the camera part of the presentation, starting from time 1:25:
