Fuel use would be hilarious, though. Also inevitably some insane person is going to make a 20,000t battlecruiser using 100 fighter engines. Sure it might go through an entire gas giant worth of sorium in one flight, but it won't get hit! And that's just getting silly.
Fuel use. Precisely that.
100 fighter engines gobbles fuel... well, like 100 fighters. At 7800% fuel use, 90 000 litres will give you 48 hours, on one engine. (a current FAC design I have is 20 days at 780%)
On 100 engines, that ship sucks 4.5 million litres of fuel in two days. Exactly how is this useful since all that engine space you saved gets stuck in fuel tanks and more? (note: 4.5 million litres of fuel = 90 fuel tanks = 90HS)
If you want to limit ships, assing a delta-v maximum that decreases with size and increases with armour. (bigger ships have a larger strain when the engines at the back thrust, since they presumably have a larger hull and stuff that sticks out the side will suffer more torque)
Use that for the checking against hit rate as well. Not sure if we want to deal with acceleration but the fuel use is already too insane.
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Another suggestion:
More than one engine type allowed per hull.
The ship has to gain a window the arranges the preference of engine use wrt speed.
If hyper is possible, hyperengines get the hyper multiplier to power. (and likewise higher efficiency)
eg.
Cruising
1st, Fuel efficiency: Uses most efficient engines first, then progressing downwards.
2nd, Thermal emission: Ties are broken preferring lower thermals.
Stealth
1st, Thermal emission
2nd, Fuel efficiency
Then we can do things like stick a gunboat or fighter engine on a normal military ship and never use it during cruising, but in battle there's the option to "go to flank speed" and burn more fuel.
Would totally do that on bigger ships. A block of high power/weight engines for just that little kick when you need it, but your strategic movement speed is much lower.
Like using two military engines per 10 ktons, plus 10 gunboat engines which are usually not running. When battle is engaged, go to full speed and guzzle fuel for the half an hour or so.
Also has other things like attaching a tug boat to a FAC, and thus saving fuel for long hauls. Cruising engine attachments. Hyper engine attachments.