Heck, Code of Honor and prejudiced are just a free points for actually role-playing a character.
Prejudiced is far from free points. I had to walk away from a meeting with a Johnson so as to not impact it negatively.
Also, you mention allergy and code of honor yet talk about free points for missions: Allergies MUST be easy to target by the GM for Missions, and Code of Honor is banned.
I wasn't referring to the SRM living campaign but pre-written adventures in general, which do not have a one to one relationship. Even if we talking SRM I still think many Allergies don't make it into play regularly and as long as you aren't the face, not seeing the Johnson isn't a big deal.
But regardless on your position as it pertains to free points all my other statements about how much a player can get shafted in the long term stand. This is especially true for negative qualities that the GM assigns after a mission begins; you don't get rewarded for getting the quality, you don't get rewarded when it is used to screw your party over, and you have to pay twice what it would normally cost to get rid of it.
I really do think that getting paid as a negative actually affects you is the most fair to everything involved, the player, GM, and game balance in general.
If the GM lacks the ability to introduce some extra factor into a written adventure, he's not fit to be a GM. And you are now adding conditions to when Prejudiced is 'free points' where before you just said free points, period, so honestly I think you're just exaggerating and using a wide blanket to cover characters who actually are decently-built rather than just going for free points. At which point you could have expected you'd be insulting a few people, really.
Hell, I am using Prejudiced(Biased, most corps) rather than Prejudiced(Biased, 1 corp) even though the difference doesn't get me free karma since I am at -20 from the other three. Being blanket-labelled a free-point snatcher at that point, especially with 11 Negotiation/Etiquette/Con dice on a Street Sam, is rather offensive.
First I really find your insinuation that I would resort to insults if I find myself unable to defend my points in an intellectual manner insulting; please don't make statements about what you expect me to do based on what other people have done.
Now that that is hopefully clear, back to the discussion at hand. The first line I mentioned free points and prejudiced was "Heck, Code of Honor and prejudiced are just a free points for actually role-playing a character." (go check if you don't believe me) That right there is a qualifier on the free points. They are free IF you Roleplay, you know have a character with a personality and actually act like that character you created. So my saying Non-faces don't really get punished by having a prejudice is not any more or less restrictive than what I said the first time. I also know a lot of GMs who due to time or whatever reasons rarely have a chance to edit a pre-written mission specifically to include character's negative qualities.
I will say I had no intention of insulting you or your characters, I don't know what type of characters you play but in my experience I have never seen anyone who would fulfill a face roll take any negative qualities that would harm the interaction skills. No offence was intended, but that is the reality in my area.
I'll point out, yet again even if we don't agree on the free points, the getting shafted for negatives on the long term and those handed out after character creation is still there. I would even argue that my statements about how royally screwed players get by GM handed down negatives is rather indisputably true.
Heck, Code of Honor and prejudiced are just a free points for actually role-playing a character. The Poser qualities rarely affect the character, especially if they manage to keep their secret. It is very easy to scrounge up a good 10-15 points that would rarely if ever affect the character in any pre-written missions.
I like the fact that you get "free" karma for Code of Honor and Prejudiced. Essentially, you're giving yourself a disadvantage when roleplaying your character with a prejudice. To use Michael's example, his character has as a background that he doesn't like (most) corporate types. He'd roleplay that regardless of the mechanical effects, which is a serious drawback. It should be worth points, and with the Prejudiced quality, it is - with added mechanical effects to be used for rolls and such.
As for the Poser quality, it does rarely affect the character if they manage to keep their secret - which is why you introduce opportunities for people to find out that secret.
I personally like those styles of disadvantages too, I just think certain disadvantages are inherently better than others because either they are part of your character regardless, or they are unlikely to come into play. It reminds me of the old Champions game. You got a ton of points from disadvantages, but half of those were mental ones that were just there so you actually roleplay the character, some were things that rarely come up, and then you had a smidgen of those massive points that were actually harmful.
I'm not saying a character shouldn't get rewarded, I'm just saying the up-front payment is inherently imbalanced in almost every scenario, either it rewards the player for little to no punishment or it unduly punishes the player for a pittance of XP. Are there times that it ends up being perfectly balanced? Sure, but the longer a character lasts the more likely it is that they will have been punished more than the points they gained for taking a disadvantage. it becomes automatically true in cases where they want to buy off the disadvantage and in the case of GM handed down disadvantages (exceedingly so at that point). Rewarding a character as a negative quality affects them is a way that is, by nature, balanced because they are rewarded as much as it affects them, both in the short and long terms.
Onto your other point though, I also disagree with the current system, where you can get disadvantages in play with no further benefit. It's fine that events during play affect your character in the long term, but in the current system you only get negative qualities for 'free' - if you can get those for in-game events, you should be able to get positive qualities for in-game events too (without paying the karma). Or alternatively, you should pay/get the karma for both. I do understand why they did it the way they did though, since the systems above are easily abused. Of course, if people abuse that, the proper resolution is hitting them with blunt paper-based objects, but I get that the rules should make it hard too.
Personally, I'd prefer a system where you can get negative qualities for free (eg no karma benefit) - either during character generation, or later during play. Since you payed no karma for those, it wouldn't cost karma to get rid of them either, although you'd still need to get rid of the disadvantage in-character.
I see Reaver and Michael beat me to the punch, but the GM can give freebie qualities. That doesn't change my view on how the player is punished more than those qualities are worth.
