So, love it.
Here are my suggestions. The 2D feel was cool back in the 90's, but I want to be able to see all of my ship. Is there a way you can make it 3D without losing that good ol' Star Control feel?
I want to see all the original ships, ALL OF THEM.
I want more classes of hulls, not just small medium and large.
I want more weapons, LOTS MORE WEAPONS.
I want more choices for batteries and recharger types.
I want to be able to mount more weapons, two is not enough.
I am not sure why you made point defense so weak. I'm sure there is a reason, but I think it should be stronger. It can't shoot down fighters and does almost no damage to larger ships.
I like what you did with the Earthling Cruiser, but...
I want all the original sounds back. THEY WERE SUPER COOL. Not at the expense of new cool sounds, just original plus new stuff.
Organize the hull pieces in the ship creator.
Keep up the amazing work. I am particularly fond of the black hole cannon, but I want all the original weapons back. After all, the game is called origins, it should have an original feel to it.
One more thing, I want to know what happened between the Orz and the Androsynth and I want to see the Androsynth make a come back. They were cool.