I've never even heard of this game, but it looks like an underwater Descent or Freespace (i.e. pretty cool). Question is, how's the joystick support? I did a quick google for an answer and I found that apparently the settings for axis get swapped up between missions or something.
Is that still the case?

If I have the time and I remember to check it later, I will. I have a Thrustmaster joystick.

Thats great to hear. I'd hate it if they took out the only feature that I'd buy this game for.
Does the game support stick twist and throttle?

Throttle yes, twist no.
I get the feeling the game was designed for a mouse first, as even though I myself am using a joystick with it, the "feel" isn't quite right, even with a lot of tweaking to the sensitivity.
As for the game, yea, it's closer to Descent than Freespace. I wound up copying my Descent control scheme for it, as well.

So far I've only tried it with the mouse, and it seems like it was made for a keyboard control scheme. Had a hard time getting used to the non-smooth turning.

and how'd you get it to register it? cause im using the same joystick and its not picking up anymovments at all.. :'(

not sure if your all speaking of the first game or the second but I have a saitek cyborg x/mad catz f.l.y. 5 and aquanox 2 and its a no-go I guess the flight-stick's too new. :(