Though I love the idea of hang a "cruise" drive, and a "combat" drive (with a comparable efficiency dropoff)
More than anything... wouldn't it totally eff up balance?
Even if your "afterburners" are something built into the engine but run off a separate tech that gets higher... What's to stop players from making fighters, with maxed out engines, that then have another stage above that. They'll be able to outrun missiles like nothing (though that would be entertaining). And late tech ones will be speed of light. Actually even normal ships would be able to readily close the gap with missile speeds.
But if you take that away, make it so that even with the "combat" setting, you can only max out at 3x normal powermod for your tech... Now you're just going to make all your warships move at fighter speeds while in combat, and fighters will slip into total worthlessness.
Personally I've always thought that everything in game is a bit too fast though. And the disparity between ship speed and missile speed was too small at the low end, and way too high once you start getting 6x mod missiles. Missiles themselves are a little odd, as speed is so much more important than maneuver rating, since it protects the missiles from defenses, while maneuver doesn't. I mean who actually puts maneuver into their ASMs, as the 10 points they have by default are almost always more than enough. And missile armor's continued worthlessness doesn't help.