All ship configuration items, as well as ship controls display & power usage have been moved into the new "Config Mode".
Now you can have AI decide which controls to bind to what thrusters by entering config mode, selecting all the thrusters on your ship, and clicking "Auto-assign Controls". As well modes (i.e. auto tracking & mouse tracking modes to turn powered hinges into turrets) have been moved into the config mode. The original keybinding mode is still available, however it is now only for rebinding shortcut keys for buttons on the HUD. Multiple components in a category can now have keys and modes set at the same time as well.
The other major change made is starting each game off with a default ship already built. Good enough to get you passed some of the easier enemies, and with a little work some of the harder ones with more powerful weapons to salvage. This will be especially useful for people playing Rogue mode, as you won't have to build a new ship each time you die and are forced to start over.