There's a lot here, and I'm not playing this game again any time soon to check your instincts vis-a-vis BTL subplot, Universal Brotherhood, etc., but there's one part of your post that especially stands out....
You know how using implants lowers your essence score subtly suggesting you become less spiritual or emotional (in the case of Glory)? This idea of changing your body making you somehow less human doesn't sit right with me.
Uh, welcome to cyberpunk. You must be new here.
What about people with disabilities that need those prosthetics?
What about them? Have you tried to ask any of them how their disabilities bring the differences between them and the general mass of people into stark contrast? The humiliation when people pander to them? If they lack the basic functionality to move about or engage in tasks that most people take for granted? Anyways, these types of questions are best addressed on one's own after their first experience with cyberpunk.
What about deckers that need the jack to do shadowrunning?
Yes, they get a piece of technology installed into their body in order to do a job. How much of the body that you were born with can you replace for functional, economic reasons before you start to wonder where the technology ends and you begin?
A wageslave with no implants is more human and soulful than a shadowrunner fighting against the system?
Well, shadowrunners don't fight against the system--they actively engage in assassination, corporate espionage, etc. at great risk to their lives. But that aside, IDK what the original rationale is behind essence because I never played the tabletop game. Do all humans and metahumans start with the same amount of essence? Is a certain amount of it intrinsic to life? Are there special rules for player characters because they are who the story is meant to be about? If everyone starts at the same place, you might have a point.
This is actively anti-punk and pro-conservative ideals of bodily purity. There are a bunch of other things I can go on about in the setting, for example how megacorporations becoming something akin to nations doesn't make much sense, but eh it doesn't matter much to Dead Man's Switch. I'll leave my write-up up to here for now because I have to go to bed, but I'll see if a discussion forms and continue on from there.
Putting aside DMS again because I think a lot has been said about it and most of it isn't original, I read in an interview that the term "cyberpunk" was first used as a marketing gimmick because punk was becoming a rather popular subculture at the time it was coined (by an author of a short story IIRC, but I could easily be wrong). Compare to the marketing bullshit around the term "RPG"--don't necessarily believe what you read on the box. Whether or not stories, characters, etc. exactly conform to or uphold punk ethics is orthogonal, really. When you see "cyberpunk," expect that you will see thugs, hoodlums, drugs, hackers, corporations, etc.