Flight Simulator Rudder pedals

[m_c]

In all honesty, in terms of electronics, I'd be looking at some of the flight sim forums, and any relevant Facebook groups to see how other people are interfacing sensors to the computer. From my limited knowledge of MS Flight Sim, it'll accept anything recognised as a HID device, and I'd imagine other flight sims will be similar, although there are probably options to create custom plugins for input devices.

There are lots of microcontrollers with libraries for exactly that purpose. Having just done a quick search, there is a HID core library for Arduino, but it needs a 32u4/Due/Zero board

As for encoder/potentiometer, potentiometer is usually a better option for controls with restricted movement, as you will always have a fixed reference/zero point/value, however you then need enough analogue inputs (although having checked even an Arduino Zero has 7 analogue inputs, while a Due has 12)
If you use a typical incremental encoder, you then need some method to zero/calibrate the encoder position every time you power on. There is the option of using an absolute encoder, but interfacing becomes a bit more involved, as you're then either dealing with a parallel connection with lots of pins, serial data streams, or some form of communication bus (I'm sure I've seen I2C and SPI mentioned in encoder specs)