Wouldn't it be nice if acceleration was based on the mass of your ship?
If you launched (or lost) all your parasite fighters, you could then accelerate faster because your ship's all-up mass has changed. If you fired off all your rockets, you would be better able to run for it, because your ship would be more manoeuverable. The same would be true for your foes, of course.
Related idea: Rather than a stock engine and the option of one or two upgrades, how about if you could swap out the ship's power plant completely? If you /want/ to cram a Carrier's engines in a Turncoat, go for it! It'd move fast, but not leave much space for weapons. Etc, etc. Me, I'd put a Krait engine in a dreadnought, and see how long it takes to get from Earth to the Moon...
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"I wear a helmet
But I've got a bare chest
I do some talking
My phaser does the rest
Don't like your tentacles
Don't like your face
Don't like your planet
Think I'll lay it to waste
'Coz I'm Rambo in Space
Yeah, I'm Rambo in Space"