-Breadboards for prototype
-Cables for prototype
Use this only for test, for final assembly make a PCB - order online or DIY.
-32 switches
-Shift Register IC 74HC165 How many?
Each 74HC165 handle 8 buttons, so you need four (no limit in numbers).
-6 Hall sensors (What type)
Honeywell SS495A-1 or Allegro A1324, they are more sensitive.
A1302 work but require almost 180 degrees of magnet turn, what will limit the axis resolution.
Movement in joystick gimbal is tipycally 20~25 degrees.
But instead HALL use Magneto Resistor sensor TLE5011, more easy to setup.
-6 External ADC MCP3208 One for each axis?
You need MCP3208 (12 bits) for axis that plan use above 10 bits - ATMEGA32u4 native ADC resolution - typically for X, Y, rudder axes. IMO - Are much hype about need of big resolutions, although this help to deal with axis movement limitation, e.g. use 14 bits for reach practical 10/12 bits.
Each MCP3208 has 8 inputs. So one fill you needs.
If use TLE5010/11 MPC3208 is not need, this sensor has internal (14 bits) ADC.