Vertigos are also more nasty because they prevent you from gaining Edge. With Edge benefits smaller than in the past, it's normal for many characters to not spend Edge on certain tests anyway, so that's not that bad. But you can still for example gain Edge when firing your gun, then use it after you turn your Smartlink off. But AR Vertigo will still work with commlink calls, while Simsense Vertigo will still work with smartlinks, so each of them has its upsides and downsides, and a player interested in any can pick the one that fits their playstyle best. Meanwhile, the mage won't care about AR Vertigo at all, while the Face doesn't worry about food allergies due to their Middle lifestyle allowing them easy access to decent food.
And yes, you can't force a player to kill an innocent witness. Which means you left a witness and a trail, and will cause trouble down the road. Merely knocking the Spider offline allows them to dial in backup and trigger an HTR team. Being lactose intolerant can be cheap karma, but it could also mean the GM rolls a die every time you eat to see if there's cross-contamination. Being addicted to cigarettes at level 5 means nothing to me unless a run takes me 6 continuous hours of not being able to take a breather. Decreasing my max Strength with 4 is free karma for any build that will never involve Strength to begin with.
As SR5 example I referenced SINner. Specifically the 25-karma level, which was basically the entire pool you were allowed in SR5. This was basically a death sentence to a player if ever revealed. And a GM could decide not to do anything with it, making it 25 free karma, or force the player into horrible scenarios despite any precautions they take. So I used to give the advice 'unless your player and you explicitly agree on the possible consequences and frequency of action required, do not allow any negative quality past 10 karma'. In the end, whenever a quality involves a GM making active decisions on how often and how much to harass you, it could be free karma in some games, and extremely nasty in others. There's a reason SRM banned a lot of qualities in SR5: Because to not make them free karma, would take significant time away from the game itself.
So I agree with you qualities should be balanced, but in some cases, it's a significant matter of opinion and GM style regarding consequences where the balance point should lie. So I'm going to point you at one of the most important things I ever tell any GM: If you don't like it, ban it. Seriously. If a character concept rubs you the wrong way, or you feel your game won't do justice to certain negative qualities and make them too much like free karma, you're always allowed to say 'sorry people, not allowing X'. (Example: In SR4, I banned Orgasm because I felt there were other spells to reach that effect and its description was just gross.) You're playing WITH your players, and obviously 'negative qualities should have an impact correlated to their bonus karma' is a big deal on making both players and GM treat the game as a fun shared storytelling event. If your table won't handle a quality the way you think it should be based on its bonus, do whatever you feel needed to fix that. But at another table, it might be too expensive instead of too cheap.
