LoP, I mean this in the nicest, most constructive way possible, but I've gotta say -- I feel like if I was trying to run an ork or troll street samurai in your game, I'd just fucking walk.
You've made up your mind in advance to give all these extra disadvantages to a couple specific types of characters -- mundanes with a lot of chrome, and orks and trolls -- above and beyond what's already mechanically in the setting (charisma modifiers, social limit modifiers, etc)...and I think it'd be awful frustrating to be blindsided by all this, just because I tried to play some of the classic archetypical "tough guy" characters in the setting.
If you just want a group full of elven, dwarven, and human mages, then good job, 'cause brother it really feels like that's what you're steering your players towards.
Then I would suggest that we have two different values for role playing games, that my personal preference for a more.... simulationist attitude is not what you need or want in a game. I don't see anything wrong with that.
If there's anything I do have an issue with is that it could be read that your post is in effect, I'm running the game wrong, because I don't want to support you, playing your way. That, dare I use the words, running things wrong. That because you can't see it, I'm abusing the nature of the game, stopping my players from doing what they want. Being an arse-hat GM because I can.
The way I see the world, if not the people in it, is one I can justify, many a discussion on a very philosophical level has given me the position I take. In my mind, I can't justify not having stronger reactions to cyberwear, it implies a choice to give up what it means to be metahuman, a link to the very world. There needs to be a very different cost it to, more than what the system suggests is appropriate. In a world which is equal parts magic and technology, there has to be something tangible, something that you can never quite prove, but link strongly. That's my goal with one part of, that being that people need more effort to notice them. That as they give up more and more of their soul, there is fundamentally less of them, it's harder to be noticed, they're more distant to the world, colours dimmer, music less inspiring, art harder to understand, appreciate. That one some level, everyone, even the mundanes, are aware of magic on a deep, instinctual level. Somehow they're tied in to this magic gestalt entity, energy, for good or ill even I don't know. How else could things like dragons be possible?
I'd suggest that the stable gene pool (In so far as it is stable while still providing sufficient reason to produce the mutations required to produce the sensitivity and/or potential to access magic, resonance) required to produce adepts, technomancers and mages would require this, at least on a marco scale. Then again, that level of biology, genetics is not an interest of mine, it's a field I follow only as required.
In fact the group only has one magic user, two heavily cybered up sam's, one's a troll, the other I believe is human. The final one is an adept/sneak, more sneak if I'm honest. The very point of this game world is that everything has its costs, you Run the Shadows and the best you can do is hope you don't pay the costs with your life. You find other ways to pay that bill. If you need to sell people out, you make sure that cost doesn't get back to you. You find others to pay it for you, make sure it isn't too high in the first place.
I'll be honest, I may bring a certain, anti-augmentation bias to this game. I'd rather see players be smart, use the assets and contacts they have, subcontract jobs out, avoid trouble at all costs. One piece of advice I will give them is keep two go bags, one if they're on a run, the other if the run goes wrong. My players will help me set the tone of the game, if they want to just keep augmenting themselves, they will pay the price for it. As the book lists and more subtle ones as well. Not only that, there will be bad reactions to wizards, the more out there something is, the more the world will push back against it. Racism, supernatural abilities, correct me if I am wrong, but has not Egypt in the game setting effectively outlawed magic in its entirety?
This is not a happy setting, it's not even a neutral setting. It's a meat grinder of a setting. The nicest people you meet are the ones who simply don't care about you at all. If you're playing it as anything other, you really don't know just how bad it is. All of the data that's collected would have given the Stasi a wet dream, a full month of them. Runners can't be stupid, yet some of the community reactions to it are that it is exactly that. The corps are borderline criminal organisations at best, if not worse. You can count on the mafia, to do and be things are in their interest. The corps not only do that, but actively support each other in doing so. They are each others biggest clients. One of them even uses nerve agents as a basic security measure and is not censured for it. It's consider their thing and they're given free reign to do it.
Hell, they openly wage a shadow war against each other, to stop one of them getting enough power to upset the balance. That for each project that does succeed, dozens if not hundreds fail due to the act of Runners. They wilfully keep a significant portion (over 60% I'd suggest, maybe even as high as 80%) of the population in poverty, enforce a class based society that values wealth and employment over all other things. If you're on the out you can never get in, about the only thing I know of that's that nasty is the caste system in India. Corruption and double dealing are very likely at epidemic levels, if not pandemic levels. If I've gotten the order of epidemic and pandemic right.
If I'm really blunt about cyberwear and augmentation, it's a cheap and silly way to play the game. It's a spiral, you do your Runs to make money, so you get more, better cyberwear. You get better at Running and to keep it up, you get more expensive and better cyberwear. It's a trap and it means if you ever get to the point of wanting to retire that character from Running, they've either got to go down to the civilian grade stuff, or forever explain how they managed to end up with some much top of the line gear.
Add in the fact, if I was to really be a bastard, I would require those with cyberwear to not only update it's software, firmware, I would also have some very intrusive and malicious code put into said cyberwear, so that if it was ever used against it manufacturer, it would be able to be identified as having been on said run, date, time, location, but would actively act as a means of the corp to gather intelligence on that Runner. If not, enough proof to either dump them in a black prison or recover the cyberwear, permanently.
Now, with the last comments, would you willingly cut off a piece of fully functional and other wise normal flesh, for something that possesses more risks, is vunerable to electronic attack, both information warfare/hacking and EMP? I wouldn't and I challenge that anyone with half a brain, under those circumstances, would also do the same. While the chrome steet sam is a classic and a viable choice in most games, it involves a level of risk that I think most would find unacceptable. If anything, I have a concern I'm actually giving the people of the the world too much credit, that while you can have custom firmware written, schematics to search for the bugs, remove the hard drives, the corps are always going to be one step ahead.
At least, if you're familiar with some of the spying antics of the Cold War, like the US leaking plans of fighters, systems to the Soviets with notable design flaws placed in them, so the Soviets would build an inferior product. I can't see why the corps wouldn't try to fake out the Running community like this. All of this is before i actively discuss the idea that the Runner is in fact, a violent criminal. Even the books seem to back me up on this.
So, again, I think I run a style and type of game that would not interest you. I don't find anything wrong with that. What I would question is what you're looking for in a game and try to offer a suggestion as to where you might find that. I would question your assumptions about the game you think I'm planning on running, there seem to be some assumptions made that I can't quite work out, understand where you're coming from.