What a great game. I'm completely amazed at what can be achieved with Ren'Py.
I love the idea of all the SF content and the theme of "Finding the Way Home". The general implementation of your ideas and the art style are also very unique. Hats off to you for that.
The added bonus of the whole Pok*mon "Gotta Catch 'Em All" like finding and creating new bot types is a very welcome one.
Having said that, I have an idea that I don't know if it had already been mentioned.
I think it would be great, if you added a factory to the player base, where one could use collected and purchased resources to build parts for the spaceship, as well as consumables like torpedoes or platings. Perhaps also supplemented by a search for necessary blueprints as in the case of the shells?
While this would require a lot of programming, I don't think it would require a lot of 3D modeling, which I guess is the most time-consuming part of your work.
What do you think? I could expand on my ideas, but I think you get the picture.