I don't see anything wrong with the ship designs re: gravity, per se. Your pilot is strapped into the seat, and we must also bear in mind that they are intended for atmospheric flight and landing on planets and stations with rotational gravity, so it does make sense to have an up and a down to the design, at least to a degree (and I'll take the remaining details that could be different on the "looks cool" principle").
Unfortunately due to the online nature of things, the cohesive approach to semi-hard science fiction has become softened more than I like in other areas. In-system travel at several times light speed irks me the most from that perspective as a result of not being able to have the dreamer time compression, but I'm not a total killjoy, so I'll suspend my disbelief that much. On the other hand, one of the most charming things about Frontier was that, except for hyperspace travel (which I grant is just a mandatory plot device for intragalactic travel), there wasn't a whole lot that broke the laws of physics blatantly. Where Frontier (et al) had Newtonian relativity, now we have maximum velocities fixed to some universal frame of reference. Additionally, the flight controls themselves and maneuverability (even taking into account "assists"), don't really stand up to the unblinking eye of physics.
All that said, of course, true Newtonian space combat just doesn't lend itself to fighters and is frankly pretty boring. I love the Newtonian-physics chases--trying to out accelerate your target over billions of miles, and then timing the deceleration to put you in range at a similar velocity--and the tactics of combat positioning in three dimensions, having to consider potentially huge velocity vectors and the possible directional changes given levels of thrust will allow, and so on. Frankly, though, particularly in one-v-many, and many-v-many combat, it really is more than a human can keep in his head effectively. And also, physics be damned, I just like Star Wars style close-range space dogfights, so despite the loss, I'll grant this is probably more fun in the end.
Still, I do dream of the possibilities of chasing a foe halfway across a solar system for (time compressed) days on end, trying to maximize my delta-v against his through clever maneuvers, predicting his course change options, and taking advantage of the gravity of massive bodies and so on. I can even imagine scenarios that, via the magic of pseudo-science techno babble, could still allow Star Wars style dogfighting while respecting this: maybe once you've closed to a particular range, you could launch some sort of "inertial damping charge" that would limit ships in its area of effect to low relative velocities, perhaps forcing them to dogfight close in with small, limited reaction mass thrusters or something.
Okay, okay. I'm ranting, and that's just not the way it is, and the way FD has worked things out is probably the best given the givens. And, of course, by all means don't get me wrong, despite losing some of the harder science aspects, it's still the best space sim I've played in ages and ages.
These space outposts look brilliant, and as more content is added and the univerese grows in size, it will just keep getting better. By the time all the expansion packs are released, it will probably be a seminal classic like its predecessors, and I'll still be playing it 10 years from now.
(Sorry about the TLDR, but I've been giving this lots of thought lately and some venues get cranky when I criticize fundamentals even coming from a default, clearly stated position of just loving the hell out of ED).