Well, the initial trouble I ran into is that Godot uses SDL-style mapping for joysticks, which is fine for the majority of joysticks out there, but for advanced flightsticks or setups with proper rudder pedals and everything, it simply can't handle it all since it has to map everything to common gamepad mappings.
For instance, I'm using a Thrustmaster T.Flight HOTAS X joystick which has FIVE axes, a hat, and 12 buttons. Godot recognizes only four of the axes by default and if I attempt to manually map in the fifth one as analog triggers I end up unable to map two of the buttons. In short, I cannot use the entire joystick with Godot's built-in handling. :(
The game I'm developing will work with keyboard+mouse or a gamepad, but because it's steeped with flight-sim aspects, I absolutely do not want to leave out people who want to play the game with advanced joystick setups so that they can have total control of their craft without having to rely on things working automatically or at a simpler level.
The plus side is I do still have my old DirectInput joystick code which I wrote years ago. With a little luck, all I'll have to do is go through the Godot integration process and then just copy-paste the whole thing!