I have the same problem. I own a T16000M (the alternative to the 3D Pro for those looking for solid yet cheap joysticks) and while it's proven to work well in other games (with an accuracy I didn't expect from such a cheap product, even though I conciously traded better accuracy over more and better buttons when I chose this over the 3D Pro), whether they're newer like Elite: Dangerous or older like the re-releases of the Star Wars and Wing Commander (which this seems to resemble) games on here, this game refuses to recognise it, sadly.

Update: well, I just fixed it. I removed my gamepad (a DualShock4 acting as an Xbox 360 controller with DS4Windows) just in case since conflicts are common with multiple controllers and then I also set the "preferred device" from the T.16000M's "Advanced" section of the "Game Controller Settings" under the "Devices and Printers" part of the Control Panel in Windows 8.1 to be the T.16000M itself.

So yeah, find the corresponding "preferred device" setting for your OS and hardware and go to town choosing your own joystick there.