No matter how we look at things, the simple fact is once a capital ship's engines are taken out, it is essentially a sitting duck. If enemy forces at that time isn't enough to take it down, additional reinforcements will. I can understand the decision behind thrusters being connected to engines but taking out engines is way too easy. I am deviating a bit from the thruster discussions but here are some suggestions.
Have 2 modes of engine operation, normal/travel mode and combat mode.
In combat mode, I imagine engines "recessing" into the superstructure or armored cowlings coming out to cover and protect the engines giving them additional protection at the expense of reduced forward thrust performance. In addition, in combat mode, make the "afterburner" boost more effective like 150% to 200% of combat thrust at the expense of lost shield strength. At the moment, there is no benefit at all in engaging boost for the majority of capital ships. You just lose shield strength over nothing. Combat boost thrust should be tactically useful (with a corresponding tradeoff like losing shields). This change will make it more interesting to make tactical decisions/tradeoffs when piloting capital ships like destroyers. Having combat mode for engines means thrusters will also work longer.
In normal/travel mode, the engine is out of the superstructure (comes out if transitioning from combat mode) as it currently looks in vanilla, or the armored cowlings recess back to the superstructure. Then it essentially performs like vanilla. You can even tie in the travel delay to the time it takes for the engine to transition from combat to travel mode. That would look cool and would give another meaning to the wait/spool up time for travel mode to engage. You can even make it so that engines in non-combat normal mode would be 50% out of the superstructure, 100% out for full travel mode. Visual indicators would be nice. It adds tactical options like, ooh that destroyer is not in combat mode, we have xx seconds to ambush and get that engine before it goes into lockdown.
Lastly, in combat mode, the recessing into the superstructure of the engine or deployment of armored cowlings make it so that the only way to easily take out an engine is if we shoot it from directly behind. You can then introduce a mechanic wherein the thrust wake damages shields/hull if we stay on it for too long. Make it difficult, but not impossible. IT IS A CAPITAL SHIP for crying out loud.
At the moment, it is laughably easy. I can take down a Xenon I with just 2 ships, a fighter to take out engines (no thrusters too so dead in the water), and a big boy with guns outranging the I's L turrets. Again, once the engines are taken out, its just a matter of using guns with a longer reach and staying out of range while you pound it to entropic oblivion. It gets boring after some time. These proposed changes introduces a bit of uncertainty and choice: shall I take out the engines or brute force my way through it? At the moment it's always, take out the engines dude, duh?!
If something like this is implemented, then flying solo in a fighter trying to take down a capital ship's engines won't become a chore. Of course there is always the option to brute alpha strike your way to victory but winning in other ways should be challenging and rewarding.