I've talked a bit about this in the discord, but I don't know if you look over there for this sort of commentary. I don't want to read all seven pages of this, so excuse me if I rehash any points already made, or staff's position on this has diverged and the question has become something else.
I played constantly during the old days of full guilds, and was really disappointed by the change when you all worked together to separate them out into classes. I pay a lot of attention to the skill effects and try to infer what staff are going for when they make changes overall to skill levels or what is allowed within each class.
I'm mostly going to talk about stalker/infiltrator/raider in this case, as I have the most experience with these, and given the game is centered around a post-apocalyptic desert world, and surviving within that desert world, I suspect you will always see the majority of the playerbase playing these three. This is especially always going to be the case where any sorts of mages are concerned, as you already made the mages a subguild, and that means for any survival ability at all, they are forced to play in these without being willing to dedicate many hours each session for play to accommodate the demand of resources.
The change from the old guilds to these classes was a straight across nerf to both 'guilds' that had combat and stealth. Staff wanted to separate out ranger's maximum utility and also fantastic stealth/scan, on top of it's great combat skills. They also, in the process, wanted to separate assassin's high stealth/scan from its high damage dealing potential abilities. This might seem long winded, but it matters because looking at where we were is important as the game's setting has not massively changed, and much of the game is designed around these things.
For the sake of this argument I'm going to ignore any talk of 'starting point' changes of previous guilds/current classes, or the branching points, because neither bothered me in the old days, so they certainly aren't a 'beneficial change' to me now.
Stalker/Miscreant were the two new classes that essentially replaced the wilderness/city stealth-utility function of the old ranger/assassin. You took away two weapon types from the ranger stand-in, or forced players to go infiltrator and drop their stealth/scan. The loss from going miscreant compared to assassin was massive. The world hasn't changed overly much for requirements of a class to survive or do certain things in their given environment, but their skill set has.
Giving Infiltrator/Scout the high sneak is great for combat people. All this change is going to do is send people that way. The majority of your playerbase is playing a wilderness class. It's Armageddon. That's the world you live in, most people are going to play what makes sense ICly. So what happens when you inevitably force people to play scout more by giving them the max stealth? Now, all stalker has is more manipulation skills, and...scan? So few people are going to pick that in comparison to Scout that you'll just have this 'issue' all over again on the other end. Few people will be playing the builds with the needed scan (only stalker essentially) to scan-see the mass of scouts (not willing to deal with the loss of both stealth and combat to get it) that it creates a sort of feedback loop where more people play stealthies and get away with stuff.
If miscreants are an issue, because their combination of high stealth + manipulation, that's going to come down to a few things. Players should accept being stolen from at times. Not constantly, and not indefinitely as it may happen currently, but it can happen. Thieves should have actual danger of being caught even if they're a stupid high agility elf with high skill. There should be timers put in place to how fast you can attempt pick-pocketing. I don't know how you'd do it, but if a guy is sitting close to you and rifling through all of your things over and over, obviously that's bad. Address this on a player basis, not by attempting changes.
If your hope is to bring more people to playing infiltrator/scout instead of miscreant/stalker, while exchanging their stealth skills will do it, it won't fix a thing. It'll make people see even fewer stealth types doing stealthy things. More people will be complaining.
I don't agree with what you're attempting, but if you wanted that 'balance', you could take away maxed stalker/miscreant scan and give those to the one-up combat builds, but you're just going to essentially recreate the same issue. It will be to a lesser extent with the scan-flip though. At that point, the end result is still going to be no one's really playing those classes you nerfed, and you wind up with everyone playing infiltrator/scout.
It's a world thing. And considering some people come to the game to play stealthy fighters, the more you diminish these things, the more you lose them. I think it's better to stop nerfing classes because you don't want everyone playing them, and focus on how to make other classes better without impacting the popular class. Let people gravitate away for good reasons, not negative input.
Skills are not a 'resource' that staff need to be spare with. You have an infinite number in your bag of code. So, instead of 'taking' from anyone, why not just boost some classes or add skills to those that encourage more people to spread? This isn't some grand resource balancing act.