I'm not sure if any of the devs ever played it, but I believe the most awesome space-combat game ever to hit the market was Nexus: The Jupiter Incident. If any dev has never played this game, I invite you to please find it, (if you can) and play it. This game broke ground on a few things that I thought made it both immersible and believable.
First, was the physics. If you got too close to a planet, you actually had to use engines to escape the gravitational pull or use your IP Jump to get out (Inter-planetary engines/ie warp). If you didn't, you started taking damage and/or you would eventually crash, especially if you had a very steep orbit. But that wasn't all. While using thrusters and then "cutting" the thrusters would allow the ship to continue traveling until reverse thrusters were used. I understand this makes the game more complex to some, but it is a "manual" mode that could be added to player's space experience as first-person was used in ground.
Secondly was the UI and the amazing amount of control you had over your ship, shuttles, and fleet. Looking at some of the screenshots I disclosed above, there are a few shots of the UI that would give an idea of how the system could work for groups -- allowing any group member to target any ship in his group for heal or buffs. And with as powerful as attack ships are getting, this is becoming more and more of a need and necessity than a mere desire. But that wasn't all, the captain could see a live read out of what was being targeted on his ship by seeing a health indicator of the subsystem that was being targeted by enemies allowing him to divert auxiliary power to that system to prevent it from being disabled. This is another feature that I believe would be a healthy addition to the game.
Lastly was the game-play. Unlike any other game out there, this game was very intuitive allowing you to use different abilities for more than just damage or a preemptive measure of damage -- it allowed you to completely take a ship offline or hack the ship to work for you. For instance, using your sensor scans, you could see the subsystem health on the ship, so you would know if you were correctly targeting the right systems. Some system would automatically show up as they were used, but sometimes reserving a weapon that you wouldn't fire was a great way to have a "backup" weapon should the others be taken offline. You could also take the weapons of the enemy ships offline to prevent them from further damaging you or you could take their beams offline to prevent them from targeting yours. Intuitive does seem to be an understatement.
I understand you're not in the business of copying games, but I do believe that this game can be a great resource of getting inspiration to what would be healthy additions to STO.