I think negative traits split into two camps, as do many such rule designing issues. One camp is the universalist approach, where there is some sort of mythical game balance with implied or explicit mathematical formulae behind them justifying each plus or minus to a nicety. The other approach is ultimately to ignore game balance completely in favor of the story telling. The "balance" in the latter approach comes down entirely to why the character is described the way they are.
Breaking Bad as an example.
Universalist Church of the Eternal Balance: the main protagonist is dying, has self doubt, is disrespected. So he gets more pluses, like bonuses on his skill rolls and a unique item - blue drug. And so on. This sort of game design is like a crossword puzzle.
Story Telling League of Balance Ignorers: it makes no difference whatever whether he gets pluses or not that somehow "equal" his negatives. He's dying, and WILL die. He's disrespected not because the world is unjust but because, as later events show, he is a sociopath and probably was from a surprisingly young age. He has the negative traits his player chose because they are what defines this character. Sure, it gives him extra picks of good things. But whether those extras are chosen or not, this is a negative, destructive character, and nothing is going to change that or make him more "playable".
I take the latter approach strongly in my own game design, having wasted years of my life on the Church of the Eternal Balance. It's just less fun to always have it balanced. That's how you get roleplaying turning into sad wargaming, in my experience.
It always comes down to what the players as a group want to do, and it always should. Also the game balance concept itself arises from the "one person runs the game" school, which is the overwhelmingly dominant school. But it truly isn't the only way to do it.
Rather than endless examples of a winged orc hunted by a group of sages who want to dissect him type characters, a better test for negative traits is to make a character like the protagonist of the noir film DOA. There's no last minute cure and he doesn't have a long life. Less enjoyable to play? Or strangely liberating? Damned hard to balance that one out though!