When it comes to controllers everyone copies nintendo.

[senseinobaka]

To correct the OP

Nintendo's innovations in control include the following:

D-Pad - and their design remains the best till this day

Shoulder Bumbpers - From SNES pad

Button layout - The SNES pad is still the gold standard in controller design. Look at DS3(which is an snes pad with grips) and the 360 controller.
Analog THUMBstick - Atari had an analog joystig, but due to it's unwieldedness it never caught on. I read somewhere that the thumbstick came from medical technology that moved things accurately in 3d-space, which is something the 64 needed. This follows Nintendo's using "mature tech in compleiing ways" philosophy. Again, the thumbstick design is gold standard now.

Accelormeter/Depth perception/and IR control - The wiimote amalgates 3 mature techs that have been used seperately in control before, but never together. By being innovative, nintendo was able to make a motion control style that actually works well and completely. And, you can bet what ever you want... but this motion sensing trifecta will be standard in coming gens. .

Force feedback - not only being the 1st with it, but routinely they are the first to use it in compelling ways in software.


Innovations that dont belong to nintendo that are routine now:
Shoulder Triggers - Sega
Analog Buttons - Sega
Dual Analog - Sony