There seems to be a feeling here that 'interface' is a secondary part of a game's design, something you can bolt over the top of a finished engine to suit the player's tastes in the same way that you can offer redefinable keyboard controls. I don't believe that's true, I think interface is the most fundamental part of a game's design, the most important to get right as early as possible, and that it dictates the possibilities and limitations of everything that can then be built into the game's world. I believe Star Control was a hugely successful design because it started from the simple, clean and proven game mechanics of Space War and Asteroids, and built up from there.
Sedodes, you make a key point when you mention predicting a flightpath. This would be the most difficult thing to get right in a 3D space. In Star Control I and II, the player can predict flightpaths at a glance, taking in range, angle and speed of approach, and develop a gut feeling for when to fire. The problem here with 3D is that our computer screens are 2D, and don't give the player a feel for such things, thus distances in numbers and predicted flight paths overlaid on the HUD by ships' computers. For me, this loses a lot of that visceral, seat-of-your-pants dogfight feel.
MrMarch, are you sure about the Homeworld thing? Homeworld had a fantastic interface.. For a 3D strategy game. It let you swing the camera around like a blue-arsed fly, zoom instantly in and out from long range scanner to pilot's eye view ranges, set up cinematic angles from which to passively watch battles unfold, and pause at any time to analyze the situation, consider tactics, and change orders. I doubt much of that is compatible with fast-paced arcade combat.
Halo vehicles, though.. Hmm. That recalls the interface from Outcast. Allow me to describe. Outcast was a third-person FPS sort of game involving combat against groups of fairly intelligent and well armed lizard guys, with a tendency to work together in packs, make good use of terrain, and spread out to surround the player. Kind of a prehistoric version of Halo in that sense.
Anyway, the controls: It was primarily mouse controlled, moving the mouse swung the camera around behind the player, turning his torso (And gun) to face the same direction where possible, while the movement keys caused him to run forward, back, sideways or diagonally relative to the camera. This allowed you to, say, glance to your right while running, by swinging the camera left while switching from 'up' to 'left' on the movement keys. It may sound a little clumsy, but was actually very natural, and allowed for a lot of fast-paced running around and dodging during firefights without disrupting your aim or running you into walls. Also, the constant parallax movement made up well for the lack of stereo depth perception.
So how about this, third person perspective with the player's ship centered at the bottom of the screen, moving the mouse swings the camera around as in Homeworld and Outcast, while the direction keys turn the ship to that heading relative to the camera, and thrust. You'd need a 'face camera without thrust' key as well, possibly the right mouse button, or 'centre' movement key. A 'track enemy' toggle could then be added without affecting the other controls, although I doubt it would be necessary. Still going to need a HUD to aim the weapons, though..