Wow, thanks for the detailed feedback, and I'm glad you loved the game!
Funnily enough, when I was working on the game originally, I did have it that you had 'slots' for your upgrades, and you had to choose what you had equipped at any given time (E.g. Alien/Terran/Machine eyes), and a rating of how much of that species you were at any given time (To enter a settlement, you needed to have 50% or more of that type of upgrade attached).
In the end, I got some feedback that it was too complicated, so I ditched it and went for the current system. I was also worried people would get annoyed having to unequip and re-equip everything just to continue a quest, or feel locked in to a build they didn't like just to finish the end game. It was also going to make balancing each build *tough*.
I'm trying to incorporate some more of the upgrade stuff into 1.2, but I won't oversell it, since it's really only some scene variations. It would be cool though if the fact you can shoot spider web from your hands, or sense magnetic fields, came up more often. :)
Checking in on main characters outside of quest events is something I'm trying to work in to 1.2 or 1.3, since I've got some ideas. I'm fighting burnout a little bit on 1.2 right now between writing new memory scenes, book scenes, and chain events, so I'll see if that gets scoped for the next release.
Thank you again for this wonderful review, it made my morning! <3