I really enjoyed playing this! There was a great gameplay loop, with playing, choosing an upgrade and then upgrading your ship. Each level you really felt like the ship improved an you got further in the game. The music and sound effects were also great and fitted the atmosphere very well.
The low-res style was really cool, but sometimes it made it hard to read the text. I think it would help if you either increase the size of the text, or choose a pixle art font that matches the resolution you are going for. I often make pixel-art games, and this is one of the things that is always really tricky to get right >_<
And secondly, I think the balancing might need some work. For me the first levels felt really easy, and the upgrades felt very powerful. For example, in my first run I got a package of three shields. This was extremely powerful, because I could protect myself from all sides. However, the boss was suddenly super difficult and I did not stand a chance. Of course, this was just my experience, so do with it what you like :D
Finally, I did not fully understand how the maximum number of modules worked. I noticed that sometimes I could put an extra module on my ship, whereas other times I could not. I saw the number in the top left, but this one often gave me some weird numbers, or did not help. (Like, one time it was -1, and another time it was 2 but I could still not place any modules). It was also not totally clear to me what some modules/upgrades did (like the ghosts, or the cats? I did not understand what they did).
Anyway, I hope you don't think my feedback is too harsh! I really enjoyed the game, so I just hope that telling you my epxerience helps you create a better game in the end. Do with it what you like :D I want to stress again that I had a great time playing, and I really hope you will continue to work in it. Thanks a lot for making this :D