You are missing the point Mara.
While an individual GM can work with his players, and account of such negative qualities (or he could ban them too, as all positive and negative qualities are still under GM permission.) The Mission writers can not design a mission for every possible combination of archtype coupled with every possible PQ/NQ combination.... and some negative qualities are very hindering.
Then you add in the fact that at Missions play, you generally don't know your fellow players or GM. If you allowed everything, you would/could end up with even more.... how to say this diplomatically?
"More whiny, pissy 'special snowflakes' that whine, cry, stomp their feet and scream at the GM to change everything so their little snowflake isn't left out" assholes disrupting everyone else's time and enjoyment.
Don't believe me? There are more then a few threads here that point to attitudes of this level even with the restictions. Imagine how much worse it would be if they didn't place some limitations.
Sometimes, things have to be cut to promote more unity and structure for everyone's enjoyment, even if it seems a little insensitive. (And for you Sterling, I can totally get your curiosity as to why they cut that NQ for missions play)
I have often stated that I don't play missions. And that is not because I don't think they are good, or I hate the limits they place. Its because I tried it 3 times for 4e.
One (IRL) broken nosed to a snowflake ended one game 30 minutes in. (Boy that felt really, REALLY good!!!)
One game ended in a screaming match between 2 players.
One game end with the GM saying "Fuck you all, I'm outta here!" And we went for beers to discuss the (in the politest way) fucking self centered douche bags that made him walk out half way through the run.
So yea. I don't play missions because the 3 times I have tried, have ended in police charges and wasted time thanks to douchebag snowflakes.... and all 3 times were with different people.
So I totally get why they place limits on builds and qualities. Maybe it will help stop people from having MY experience with missions play.