@Metric-SINISTER The ships have gravity engines(anti gravity) This is what gives them maneuvering. some are stronger than others. But they are very weak in comparison to thrusters. thrust or pulse engines and others, giving them steering advantages for high speed transports. So, if you know how thrusters work, you just lower one and engage the other and you get hard turning. then you can maneuver up and use both and get a heavy turn since you engaged both. yes, its true they should not be able to stop like they do, not without overpowering the engines for over powered maneuvering brakes. as you should move forward with thusters many times faster, an emergency stop would cause you to burnout power engines or at least over heat them and need a good cooldown in theory. That said, between thrusting and braking there should be a different of three to one. all these systems would work in this very game, very easily and effectively, but they did not intend to use this factor since they had the pandoras box component of boosting. but thats besides the question.
There is always and achilles heel(not a weakness, but vulnerable spot). This is also beyond the question, cause this can be ,,game accurate,, and only needs to follow the principles of the lore. A missile can do an easy job of assuring that this weakness is in check. just like the tractor beam is used as a weapon rather than a hauling device. So instead of having laser canons fire through ships, just have rockets fire. Solved, no? not too difficult. If they cant then survive as a flag ship, its either too weak of an adjustment or they are just need to fight harder to protect it.
Also the lasers can be a bit more stronger on all sides, but besides that with that said, the republic flag ship can be more heavy on missiles. I mean those huge antenna are good for something, if not for anything else, would make really, really good targeting sensors.