Few comments.
First of all, if the effects of gravity is being ignored, isn't it possible for the effects of acceleration to be ignored or at least reduced? I am thinking of an inertial drive, something that is in fact simpler than artificial gravity. It is simply the ability for all objects in the ship to accelerate at the same time, as opposed to the hull accelerating and pushing on your body, which in turn accelerates it, but can kill it if it is too much. A super-efficient chair strap. You still need to be able to survive the gravity, but it'll be constant over your whole body and not crushing which helps lots, though this relies on artificial gravity.
This could possibly be a tech tree on its own, where without it you can only have a max delta-v of 5x-10x of your race's gravity tolerance, but with higher tech can be more. (Or bred crew with higher g tolerance, different from usual engineering of population with lower g tolerance who colonise moons. )
Second thing I'd like to add is the concept of escape velocity and orbits. Essentially to orbit (at ground level) earth, you are travelling at 11. 2 km/s. If you leave earth all you have to do is be nudged out of orbit and you have already attained that speed, no need to accelerate from 1km/s. Well, that's at ground level. Wikipedia says the actual low earth orbit speed is at maximum 8. 2 km/s, but that can be calculated I am sure.
My suggestion is that when entering and leaving an orbit you only have to speed up from the source's orbit velocity and only brake to the destination's escape velocity. This isn't that much difference for earth, but with Jupiter having an escape velocity of 59. 5 km/s it could add up, if ever so slightly, especially since this also invokes free course changes at this (low) speed.
Now what I am REALLY thinking is that the Sun's escape velocity is 619 km/s. Starting at that speed on spotting an enemy could be a SIGNIFICANT advantage. Course, you need to be far away enough from the Sun to not be toasted so that figure would be significantly slashed, but I can imagine a starting speed of 300 km/s already being a possible consideration for advanced races, esp for black hole systems which have even LARGER time dilated orbit speeds.
On time dialation, I'd like to see military ships travelling at relativistic speeds (or very near INTENSE gravity) having their maintainance clock slowed. It is unlikely to often happen so would be a small check with usually a small effect, but it is just that extra touch of detail without adding extra micro-management that Aurora is famous for. Might happen more often and be more relevant to inter-system travel which by necessity is FTL, if jump points aren't used.
On to accelerators. You have mass drivers, why not a mass driver for a ship? Imagine a launching platform with intense engines that can throw out fighters or even larger ships at 2000 km/s or more. This could even be miles and miles long to allow less of a gravity delta, but would likely rely on inertial and gravity technology for anything manned. Once you have accelerators though there is no reason you can't have them 'catch' too, reducing the delta-v needed for ships to leave and enter orbit(possibly at a fuel cost). If this is something that like shipyards need to be built or tugged this will mean an advantage for any race acting in its 'home' system, though a critical piece of infrastructure to reduce the costs of running an empire. I can even imagine engineless ships being flung intra-system, accelerated and decellarated only at the endpoints by these accelerators.
Now extending accelerators to missiles. There's no reason for missiles to start at the same velocity as the ship, when the ship can offer a boosting thrust. Since missiles are unmanned these accelerators can be shorter and more powerful than for ships. This will directly affect the fuel needed for missiles and through that their range. This will also mean that missile launchers on ships will have more tech variables than just reload speed and size and be something that actually needs to be updated with advancing technology. Such missiles can potentially operate with no fuel at all, having only enough to maneuver and course correct as it approaches its target. Also that the same missile launched with two different launchers can act VERY differently, either a powerful launcher with more range and less agility(harder to course correct a faster object) or a less powerful launcher with the reverse. I am unsure whether this extra complications of an already complex missile design system is needed, but it follows naturally from the accelerators idea above.
