It's nothing at all like real flaws because they don't actually affect you mechanically at all - they just exist to encourage you to let the GM make the plot actually matter to your character by handing out cool bonuses in the times that they do come up.
I agree with everything you've said except this part. Supe's Kryptonite allergy and magic weakness is covered by the system, as is the Human Torch's getting doused removing his ability, and numerous other mechanical effects.
As to defense for BigGuns statements, how often do you get players who take some mild allergy that barely comes up or picking uncouth or something else that almost never affects them? 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.
In Shadowrun if you get 15 points of negatives then your GM has carte blanche to bone you as much as they want, and you don't get jack from it. If you want to get rid of it you have to pay double the amount you gained, meaning a minimum of 6 sessions (using standard rates) to get rid of those qualities, If your GM even lets you. Oh, and the system has built in things where you get NEW negative qualities and have NOTHING for them so you are really boned because you have something that screw you over, didn't get anything for it, and if you want to get rid of it you have to pay twice what it would normally cost so you get REALLY boned every step of the way.
Now compare it to M&M where you take negative qualities with the possible reward of better dice rolls and all the other things that Edge provides. If you get tired of that negative then you resolve it in character, and it goes away without paying points. If your GM gives you one then you get rewarded for it whenever it comes up and if you can resolve it whenever you want to get rid of it.
If you get rewarded up front for negatives the short-term benefit is there with little to no disadvantage but if you look at the long-term you are getting screwed over royally for a pittance. Getting rewarded as you are affected by something rewards you in proportion to how much it effects you in both the short and long term.
I'd say that the being paid AS something effects you is WAY more fair to the player and GM.