Having the items give upgrades to the ship was in the original idea. I decided I needed to get a playable version out, so a lot of stuff got cut. Now that a playable version is out there and I still want to make something bigger I should revisit old ideas and new ones to make the game more fun, because the game definitely needs more to it.
I guess my thinking now is to have item slots on your saucer as well as the mothership. So you will have items that repair the mothership and items that get attached to your saucer and give a permanent upgrade. The battery increasing the max power is a good idea, and an item to slow the amount of heat you get when spotted. There is so much potential for cool items I need to decide what adds the most fun, and go from there. A bucket of paint as an item to change the color of the saucer needs to be added, Nice idea.
I copy pasted all these ideas to a big text file I have for future consideration, but for this week anyway I am just trying to tighten everything up, so the game is in a solid place before I start adding things. Thanks for the continued feedback!