Umm actually Atari had an analog controller long before it was ever dreamed up at Nintendo. And strangely enough Sony released a dual analog flightstick a year before Nintendo introduced it's Nintendo 64 controller.
source: http://en.wikipedia.org/wiki/Analog_stick
History
"Many, if not most, 70s consoles featured an Analog Stick, see under, the VC 4000 (1978) for more info. In 1982 Atari released the first controller with a potentiometer-based analog stick [2] for their Atari 5200 home console. However, the non-centering joystick design proved to be ungainly and unreliable, alienating many consumers at the time. During that same year, General Consumer Electronics introduced the Vectrex, a vector graphics based system which used a self-centering analog stick, obviously a precursor to the modern design.
For many years, consoles ignored analog technology, instead using the digital D-pad. It wasn't until the emergence of 3D gameplay that the analog stick was brought back for widespread use.
In 1995, Sony (realizing that analog technology could be useful) created a potentiometer-based analog joystick for use in Flight-Simulation games. The Sony Dual Analog FlightStick featured twin analog sticks and was used in games such as "Descent" to provide a much greater degree of freedom than the typical digital joysticks of the day.
In 1996 Nintendo introduced a modern analog stick called a control stick on their Nintendo 64 controller. Unlike the D-pad, the control stick allowed for varying levels of pressure and 360-degree control, translating into more precise movements in games such as Super Mario 64. (Incidentally, Super Mario 64 DS was criticized by some for imprecise control due to lack of an analog stick on the Nintendo DS.)
During this same period of time, Sony was also creating a similar analog stick, based off the same potentiometer technology that was used in the larger Dual Analog Flightstick. Released in November 1996, the Sony Dual Analog controller featured three modes of analog (Flightstick, Full Analog and Analog-Off), and dual plastic concave thumbsticks, while Nintendo's controller only had a single stick."