I also noticed the issue where fighters are now slower than the carrier in some cases - this is an issue with realism in space combat because there isn't any realistic reason to use fighters in zero-g. There is no upper limit on speed for space vessels, so size isn't a factor in speed. The only reason to use fighters would be that a smaller mass is easier to accelerate and a smaller profile is harder to target, but with laser point defence and infinite sub-light fuel these benefits are made moot. Bigger is always better in space, using realistic flight models. Only maneuverability could be claimed as a benefit of a fighter, but given their fragility and the range of all weapon systems maneuverability doesn't really matter.
Additionally the problem of calculating the proper leading pip for ballistic weapons fired between two ships which each have their own full physics simulated in two dimensions is quite difficult, to put it lightly. An easier problem than three dimensions (to the guy who mentioned the X4 mod), but not really by a whole lot. Even with approximated inertia, ships in the vanilla game sometimes don't lead their target properly. Of course, if either ship adjusts their acceleration even minutely while at great distance, the entire calculation needs to be repeated. The accuracy of ballistic weapons in space combat falls to near zero in any realistic simulation, so this is pretty much as one would expect. Unless the muzzle velocity of the ballistic weapon is extremely high, good luck trying to hit a space ship that is executing evasive maneuvers. The problem with high muzzle velocity is of course the recoil which results from the shot, which goes up in proportion to the kinetic energy of the projectile, but to have any kind of accuracy you'd want to have the projectile travel as fast as conceivably possible.