my first suggestion is that, when targeting a ship, the ship's 3D model would appear in the top right corner of your screen along with name, faction, shields and health, I feel it will add more atmosphere to the game, I dont know Unity's restrictions when it comes to this but I believe its possible because the team was able to create the new galaxy map, which looks pretty similar.
Another suggestion is the collision of the shields. I've had countless times where I wanted to fly close to a really large ship and take a screenshot, but the shields of the ship would kill me, is there a way the change the collision box of the shield so its closer to the ship and more tightly wrapped? I know this would require some algorithm to detect where the ships bountaries are but again I believe its possible.
Speaking of large ships are you guys going to add some sort of atmosphere effect to larger ship classes so that they Feel big and slow? I know I can just change the engines on the ship so they feel a lot slower but then speed is a huge issue. Taking EVE Online for example pulls this offer very well because it has a certain atmosphere to its ships that I'm afraid I cannot lay my finger on, maybe you know what I'm talking about I don't know.
My last suggestion is for Missions, I think it would be cool for a random mission to seige a Spacestation, where it would fire back at you and it could deploy its own ships from a pool of custom fighters that dont appear anywhere else. After you're able to damage the spacestation enough they would surrender and fall victim to the faction you worked with, lets say you have X faction and Y faction, a mission is available in X faction system to travel to Y faction system and join in a raid to fight one of Y faction's spacestation, thus expanding X faction's controlled area and giving the player some choice of who he/she wants to help.
I hope I made sense with these suggestions I feel like they're great but everyone opinion varies..