I have a couple of suggestions. I'm fairly new to the game, so it might be that I've missed something, but I don't think so.
1. The lack of versatility in cargo holds annoys me. It's impossible to carry munitions, or small craft without the ship in question being classed as military. I'd like to see the ability to carry those things in cargo bays. I know it seems sort of unbalancing, but if it was set up right, it would simplify military logistics a lot.
2. Missile launchers in PD mode shouldn't engage targets that are out of range. This is almost a bug, but not really. It's simple enough to avoid if you know it's there.
3. I'd appreciate the ability to 'rough out' ships with designed components without having to research them. It's annoying that you have to guess the final ship size, then research the jump drive, then build the ship. And if the jump drive is the wrong size, you either have a more expensive and massive jump drive then you need, or you have to research another one.