Adding a selector to cycle through detected joysticks or gamepads would be extremely useful, both for debugging joystick setups and for ease of use.

Right now it seems the joystick/gamepads are selected based on activity, however if you have a noisy joystick that is tuned through another program, the noisy one is selected with no way to select said quieter, tuned stick without fully disconnecting the noisy stick and restarting the game.

This is especially useful if you are running a full HOTAS setup that is being tuned and simulated as one controller in a program like Joystick gremlin or T.A.R.G.E.T.

When I first implemented the detection system, I already knew that this could be a problem (I had similar issues with a homemade gamepad emulator used on other games a while back).
You are perfectly right about the activity detection. While this system will stay as a default, I will probably add a "debug" menu to show all of the connected stuff on your computer (and the available axis/buttons on each) in addition to a way to "force" the mod to use inputs from one gamepad in particular. This system will work by checking the name/device ID to select the correct gamepad.
Now I can't really tell when I will release this update, but this will probably happen at the same time that I finish the UI rework, so next update I hope.