I know it would take a lot of coding changes and may not be worth implementing, at least at this time, but the engine system I'd like to see would be based on thrust/mass.
Each engine would rated for thrust produced and that would be compared with the mass of the ship to produce a speed. Fairly simple, but it makes good Newtonian sense, especially when compared with the current system.
I'm not really sure what I think about the current cap on speed for larger hulls. Is there a rational behind that, besides possible game balance issues? Reduced hull integrity for larger hulls or some such? And is it really neccessary for play balance?
I don't really think there should be a cap on the number of engines that can be placed on a hull. It would open up a whole 'nother area of choices to be made - exactly how much component space should be sacrificed for more speed?
If you have an initiative system based, at least in part, on speed, it would give faster ships an advantage but they'd have less weaponry to apply with that advantage so I think it'd even out fairly well.
It could give even more problems with the missile dance maneuver but if may even prevent some if enemy ships have the speed to close that gap despite retreating opponents.
I think, when it comes to retreating, there's no reason not to allow faster ships to break away. I'd like to see a scrolling combat screen and the ability for ships that reach a certain distance from the nearest opponent to remove themselves from combat.
If ships of more variable speed are allowed and not every one proceeds at virtually the same pace, than interceptor ships as well as raiders become possible. Add a ship or two optimized for speed to your fleet and let them harass the enemy as they attempt to retreat. Put some engine destroying weapons on them and they'd have a good ol' time!