Honestly, if I wanted to give a mage that went with sensitive system some downside in active gameplay to that drawback, I would probably send them on a run where there is a lot of anti-magic equipment, taking away their magic (temporarily) and forcing them to rely on their other skills, which can be problematic because a mage who took sensitive system is likely a very heavily focused magician, and won't have much skills outside their magic, then it would be interesting for the mage, who would have to work outside their normal comfort zone (a huge element in storytelling) and it would give everyone a goal of disabling the anti-magic objects.
How is that, in any way, a story element that has anything to do with sensitive system? All it has to do with is the person being a mage (sensitive system or not).
Magic who choose sensitive system might be accused of getting "free" BP, but think about it, never will they get fancy cybereyes or a pain editor (which would come in HUGE use for a mage). And frankly, that means that magic has become their crutch in life, it provides a lot of interesting roleplaying elements. This character cannot get any changes to their body like everyone else can, no augmentation or changes in any way, in a world where they are considered the norm in many ways. That would lead them to rely on their magic heavily throughout life, maybe even isolating themselves from society.
They can though. It's not full-blown bio-rejection. It merely halves their essence resource for
cyberware. A mage who takes it has the added downside of having magic affected more. Again, that isn't a sensitive system issue, but a mage issue.
I guess this is the time to point out, it doesn't matter whether the sensitive system character is a mundane or mage, he's the one getting picked in such a situation. Likewise, if I'm having to "randomly" determine which of the group is getting nabbed and tortured, you can bet it will be the guy with a Low Pain Threshold. I've actually seen more mundies with Sensitive System over the years than awakened.
There is after all, a point where the player will likely feel put of because you did single them out and drastically change their character, and than they might feel that your picking on their character and negatively effecting their character to pick on them personally.
Well a few quick points. Losing a point of magic is
not a drastic change. Maybe its coming from previous editions where magic loss was easier to accumulate than nuyen, but losing a bit of a renewable resource (you can keep initiating and buying up magic) is not crippling and dramatically harming the character at all. It would be another thing if it were a horribly limited stat, but even then I don't think it would be a crippling change if it's a once in a campaign deal. I don't really buy into this belief that all character growth should be both mechanical and positive development.
Like I said, I can and will kill stupid characters, and than tell the players why I did it, but I won't single them out and exploit their flaw unless there is a story reason for that character to have been singled out for that specific treatment. If I feel a player is abusing the negative qualities, or is going to, I will not let them take it.
This goes above and beyond letting players take inappropriate flaws. I have no qualms killing characters when they botch things up bad. I won't usually kill them for one bad roll, but stupidity (including lack of prep work/legwork) is the main reason for fatality in most SR games.
The point here is that as a GM, you make the story. If a player takes the time to tailor their character and point out parts of their character that are going to be part of the story, it's a GM's job to make sure they come up. If a player takes the pistols skill, I'm going to make sure there are some combats in the story for that skill to be used. Bringing up negative flaws falls in the same camp.
Uncouth is meant to be heavily roleplayed, whereas sensitive system will likely have an effect on the character and their outlook on certain things, and it does make it so they cannot take augments without paying out the nose (sometimes literally), so this effect their everyday lives, sometimes less than uncouth, sometimes more.
Mechanically it doesn't prevent augmentations at all. It just limits what is viable. A character with Sensitive System can still get a maxed out set of cybereyes or ears, a half limb, or internal commlink without losing more than one magic using only basic ware. Keep in mind it doesn't impact bio-ware at all either. In game, the character will likely be on immune suppressants and having to constantly get minor work done to remove build up on implants or on the opposite end of the spectrum, taking constant immune boosters because the augs killed their immune system.
If a character gets implanted, they lose a point of essence and magic, but they aren't likely to keep the implants they received usually. Once they get them ripped out, they will still have a point of essence to spend on ware before they lose anymore magic.
Let's also keep in mind that I have never said "A character with Sensitive System must be secretly implanted by cyber ninja mafia at some point during the campaign," I merely listed it as
one possible avenue of bringing the flaw into the story. What I've said repeatedly is that flaws should play a part of the story, and I don't think that part of the story should be passive.
Once removing the ware, the character has a hard choice to make. Does he use that essence up on new augs that he wants and suffer from it as his body fights to reject the augmentations making it literally a pain for power choice, or does he live with the constant thought that he could be just a bit better than normal with a little work done.