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It is not about fingerprint size, it's about fingerprint sizes delta before and after. Take any image editor or paint app. When you want a tiny line, you barely touch the surface of the screen, when you want a bold thick line, you press your finger harder to the surface - I think 3D Touch work the same way, but I will check that to be sure. The reason I doubt is because it could be implemented much easier, no need for extra sensors and stuff. You say fingerprint sizes are different. Yes, but pressure is different as well for different people, isn't it?

Apple iPhone 6S Technology Page said:
Retina HD display with 3D Touch
The technology behind 3D Touch starts with the display, which recognizes the pressure you apply in addition to the familiar Multi-Touch gestures you already use.

Capacitive sensors
Designed to measure microscopic changes in pressure, capacitive sensors are integrated into the backlight of the display. These measurements are then combined with signals from the touch sensor and accelerometer to provide fast, accurate, and continuous responses using a series of complex algorithms.
Source: http://www.apple.com/iphone-6s/technology/

To my knowledge, Apple doesn't have a history of flat out lying about their technology innovations. Either they don't say anything, or they give accurate information about how they've implemented a feature.
 
90% of the uses Apple showed for force touch could be done just as well with long presses.
You must be looking at the wrong thing. The "pop" of peek/pop isn't possible with a long press unless you want to accidentally trigger it all the time.
 
90% of the uses Apple showed for force touch could be done just as well with long presses.
Dang man, where were you five years ago. Apple could have really used your insight into this and saved millions in R&D cost, not to mention time. Bet Tim Cook, and Jony Ive are slapping their foreheads right now! And boy oh boy will the board of directors be pissed.
 
It doesn't make any sense to me to put another extra layer with some transparent pressure sensors between LCD and digitizer instead of just measuring the fingerprint area, but.... I'm no doctor.
My guesses: They needed to be able to detect force consistently regardless of whether you used your thumb or a finger, and regardless of you're using the full face or a side of the digit. Additionally, human fingers do vary from person to person, so what looks like a hard press on one finger might not on another.

I'm sure they tried measuring finger area first early in their r&d, but ended up deciding a mechanism to measure displacement is more effective
 
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