Hey there! Thanks for leaving the feedback - it's not a TL;DR at all, you're making good points. I ran out of time about three quarters of the way through, so there are a few things that got sort of garbled.
It's true that the "good-guy" faction comes across as a bit too morally questionable. That's one of the inherent problems with writing drone/conversion kink, I think. They're meant to be spicy, and a little morally ambiguous, but not evil. I'm not sure I struck the right balance, and that's something I'd try to workshop a little more if I was writing the game now.
The way it worked in my head is that the robotification is happening on a large scale, and has been happening for a while. The good-guy faction is subverting the process as much as they can, but they can't outright stop it (yet). At its core it's being run by actual AIs and not converted humans, and they're meant to have slightly alien reasoning as a result. I'm not sure that actually made it into the game, though.
The main character's level of free will is another one of those things. The way it's meant to work is that they have free will, with the "drone mode" just constraining their behavior sometimes. There should probably be a choice to refuse working with the good-guy faction, which they would respect. Just didn't make it in, in the end.
As for Reset Day, I kind of got sidetracked; this has been a rather crazy year. I'm definitely hoping to get something out next year. It'll hopefully have a better story structure. I'll spend more time looking at everyone's reasoning, at least.
Thanks for checking it out all the same! I found your feedback very valuable.