It seems this would be more of a scripting issue - we have rotational code in place. What we would need is a script to take into account the forward velocity of the ship when applying roll to the engine pods - the faster you're going forward, the less the pods should roll (in the case of an atmospheric fighter, at least).
Thruster points indeed can't move, I forgot about that.
Also, you are proposing actual scripting, which isn't something that most people know.
By "animation code" I meant what can be done via tables, which currently only allows "on/off" animation (it's moving from one position to another).
For this, you'd need support for "dynamic" (the more you move the stick, the more the engines will turn) animations.