I echo the previous post. I usually leave non-combats alone such as supply, colony, freighter etc. and focus on creating specialized military ships.
One tweek that I use a lot is removing the survey component from the survey ship and adding additional sensors. Creating a ship that can see many hexes to serve as a sentry. Then creating a ship with a lot of moves and a single railgun (or beam). Then when those pesky Torians start sending a stream of colony ships to your area - you can pick them off.