I'm glad the interactions between her and the computer were a highlight for you, they were fun to write, and I would love to add more of that, as well as just extra small interactions on each stage around the ship.
My plan at the start of the jam was to have a few random puzzles much like you suggest, but I was only able to get the one type working in time. A maze isnt too bad of an idea, and could be pulled off easily enough. I had a switch puzzle I was working on where there was a bunch of switches on screen, and if you flip a switch it would turn on or off the switch beside it, and the goal would have been to get all the switches turned on, but it didn’t pan out on the first go so I scraped it for the jam.
"maybe something that affects future stages and how they're accomplished? like if you repair with minimal mistakes it make the next zone easier and you get more time at the end? more mistakes could effect cryo-pod efficacy? or more mistakes could make the baseline difficulty for the puzzles higher?"
Now that is an interesting concept, but might require much more time to implement correctly. Currently that might be outside of the scope of what i want to do with this project, but ill keep it in mind
the airlock is unused, but i did have the idea of her being forced to go outside her ship and do repairs out there as well. Getting repair materials isnt a bad idea though...