I hope StarDock takes a page from the game StarDrive when it comes to ship building and combat. StarDrive is basically a real-time version of Galciv, and I think the strongest element of the game is how the ship builder impacts the tactical battles.
I'd love the new Ship Builder to allow you to actually place the types of armor on the hull in the places you want followed by guns, shields, power etc inside the hull wherever you want. What is cool about this is that you can fortify the front of your ship but leave the rear weak if you want. If the starboard side of your ship takes heavy damage then those weapons stop functioning. If you target the engines of the enemy ship it loses its ability to move. If the warp core or power plant gets destroyed the entire ship may blow up! How you design your ship directly impacts its combat abilities which was really fun to see.
If combat remains automated it would be really cool to have the ability to create custom formations for your fleets. In this way you could place your cruisers in front with your support ships behind them and maybe the fighters on the edges for the strafing runs. In this way the support ships would be protected by the cruisers in front. Creating formations that your fleets use when they enter battle would be cool. Currently any ship can shoot through a ship to target anything it wants which isn't very interesting.
Also being able to give a wide range of combat orders to fleets for when they enter battle would be great. Maybe I want my fleet to outflank the enemy fleet and have my ships prioritize certain targets. Or maybe I want them to remain in a tight formation which might limit their ability to shoot at targets but also helps protect the weaker ships. Certain formations could work better against others and help make a difference in the battle outcome.
These are just some ideas I thought would be fun. The ability to customize ships and see how your ship fights in battle in StarDrive was really fun.