The idea is simple and in my opinion those two things are currently the only parts of your ship you can't really customize to your needs. While simple this would still be some mayor project and therefore I don't think it would still fit into CF 2.0 at this stage but maybe a future update.
First thing to do would be a slight reduction in base speed and maneuverability / turning rate to all ships (or at least the ones where upgrading those two would make sense in the first place). I have a reduce of 5-10% in mind here, nothing too serious as it would otherwise affect early gameplay negativeley.
Then introduce the upgrades in various tiers with various benefits and downsides as well:
Maneuvering Thruster Upgrades
Increases turning rate in small steps (maybe 5% per tier up to max 25% - just a suggestion) while simultaniously reducing armor strength in the same amount as putting more, bigger or even more unstable thrusters on your hull would simply reduce the armor coverage or your ships and provide bigger weak spots
Engine Upgrades
Basically the same as with the thrusters - 5% steps up to 25%, again MK I to V, while reducing cargo space for 10 each tier, up to 50 as bigger engines mean more power/fuel need, therefore you'd need more space. But I'm suggesting a small reduce in armor strength as well (2% with each tier up to 10%) as a bigger engine and power core or fuel tank would be more likely to take major damage from weapos fire. This Upgrade should not affect cruise speed, as it is just perfect right now. It would only affect the base impulse speed and therefore the max speed while you're running the afterburner.
This said you would also have to adjust the current Armor Upgrades to increase the impact on mass respectiveley to simply prevent players from haveing a VHF that handles just as a LF while still being able to increase the armor. My intention here is simply to customize your favourite ship even more to your playstyle. You will be able to have a VHF that turns like a HF for example but you'd have to make serious cuts to your survivability. You could as well optimize your sluggish and slow freighter into a fast smuggling vessel or courier ship that would have more chances to get away while space is on fire - but you would sacrifice some of your cargo space. Or you could make an already agile interceptor even more agile and fast but you'd literally have a cargo bay with as much space as common wallet - which leads me to the next adjustment that would be needed: base cargo space. Ships as the Butcher for example would need some increase in this matter as it would still be nice to be able to get about 10-20 pods into your cargo even with the max engine upgrade.
These is a mayor request, I'm aware of that, but I think it 'could' improve gameplay and would provide even more stuff to eagerly search for, more possibilties to mess around with your outfit, then fail and mess around even more until you finally find your much personally golden path. Needless to say: "Need MOOOAAR UpgradeZ!!" 
Hopefully I'm not too ambitious here and you take your time to consider my request - would be so awesome to tune your engines 
EDIT: This would as well provide the opportunity to add some specialization to Liberty and Bretonia as they lack in that regard right now. The Kusari have their shield upgrades, Rheinland has it's power generators. Let Bretonia and their respective criminals have the engine upgrades and Liberty the maneuvering upgrades ad all of the houses would ever be happy to have something the others don't have 
