Random ideas.

Dual firing weapons spacing (from a suggestion by NMS).
The ability to vary the spacing between the two streams of fire from dual/alternating weapons would be very handy to allow 'fitting' of dual weapons to ships.
Possibly the game could detect weapon slots on a ship which specify dual/alternating weapons and automatically set the weapon spacing to this. Or if no specific slots then use default spacing or whatever spacing is set in the weapon code.
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Omni turret overlay (someone else suggested this - can't remember who - so no credit to me, I just like the idea).
Two options. Both are an image which gets placed over the ship image so they are visible.
Possibly a different image could also be used for point-defense devices.

Option 1 is a fixed image which could be set on top of the ship image and rotate with it (like a pteravore does). This would allow offsetting the turret from the center of the ship image if this looked better. Probably best if this is a circular design.
This would give a visible indicator that the ship has omni-fire ability and also serve as a definite point for weapons fire to originate from, as opposed to the current "weapons fire from the centre of the ship image whether it looks appropriate or not".
Not useful for dual weapons though.

Option 2 is a larger independently rotating image.
This could be used as an added device which omnidirectionalizes or 'turret'izes fixed weapons. And for dual weapons where weapons fire spacing requires a certain size of turret (more below).
A larger image which while fixed at a certain point on the ship image could rotate independently of the ship to 'point' weapons in the desired direction. Weapons fire would then originate from the front edge of the turret image. The time taken for a turret to rotate to point at an enemy could help balance the greater ability of a fixed weapon used like this. Or rotation speed could be increased/decreased by ROM or device.
The turret could automatically point to any nearby enemies or point to whichever object is targeted by the playership (ROM upgrades?). Otherwise it could either remain set at its last direction or return to a default forward direction. Or it could take time from when the firing button is pressed to rotate to the direction of the enemy.
Again this gives a defined point for omni weapons fire to emerge.
Based on quick testing with an EI200 some change to weapons fire will be needed. EDIT: There are already a couple of tickets about weapons fire and shot effects being separate and appearing above or below the ship. END EDIT. Omni fire from the EI200's laser is visible for a short distance from the firing point but then appears to go under the ship before reappearing outside of the ship image. This only happens on the long axis of the ship.
Ship image size limits the turret size. Not possible on a Hornet but a CSC could have many.
The distance between the twin streams of fire for dual/alternating weapons also sets a minimum image size. If the spacing is reduced too much the weapons fire will merge into one line of fire (assuming variable spacing as mentioned above). So there would be a minimum size for the turret image which allowed distinct streams of fire but which also appear to originate from within the turret image. And they would need to fit inside the ship image. Or duals could have their own larger turret which can only go on larger ships. The turret images need not be circular here. Rectangular or wide turrets could fire from the longer side to cater for dual weapons fire.
Could also be used on stations, especially if a fixed fire arc ability is added to them (might already be there?). These could replace or augment the existing separate defence turret stations.
Possibly weapons used in turrets (or the turrets themselves if they are a player installable device) could have a slight chance of being damaged as they are somewhat more exposed. Or there could be several turrets with different armor or levels of protection (maybe have a separate shield for the turret?).
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Multiple devices.
Launchers, shields, cargo holds, drives.

Multiple launchers would be nice.
Shields could either layer on top of each other or only cover a certain arc/section of an object. Could have shields on stations.
Extra cargo holds could be an option. Could use an additional image added to the ship, like side mounted weapons, to make the ship look larger.
Multiple drives to give either more acceleration or top speed. Or a forward facing drive for 'emergency stop' manouevers. Thrusters to enhance rotation.
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Compartment selector screen.
Or some way of visually repairing hull damage in a player ship with compartments.
The only idea I had was a deviceSelector type screen which showed the different compartments in the same way as device slots. Then actions could select the compartment and it could be repaired with - here's a great idea - interior repair patches!!