I'm really not all that great with physics, but I do know that the only place you can escape gravity completely in in DEEP space, where there are no planets or other massive bodies for billions and billions of miles to generate a grav field. Deep space is also extremely dark, because like I said all stars are extremely far away. Perhaps what limited gravity there is in normal system space still has enough of an effect on objects of larger mass to adversely effect their speed. To support my point, NASA has sent probes out into space, which should logically remain at a constant speed because of the lack of gravity, yet they are slowing down mysteriously... Which brings up my next point; there is far too much that we don't know about space to understand how everything works, which is why even Steven Hawking could not completely, 100% surely say that the flight physics of wing commander are wrong. Perhaps Capships are purposely designed to travel slower because their higher mass would mean that they would have to expend more energy in slowing down because of their inertia(which, gravity or no gravity, an object in space would have). THe lower speed could also be because a CapShip's low maneuverability would have it crashing into planets and other gravity wells and spatial anomalies because it would have too much speed and inertia to compensate. That brings up my final point; despite having sensors, a CapShip never has a 100% clear picture of what's in front of it, and traveling at extremely high speeds, with or without all that phase shielding and armor, would be lethal even if whatever it ran into was very small, such as a basketball sized meteorite. Fighters could go faster because they have the maneuverability to avoid obstacles at the last second.