I will say Design Quirk is in my top three of traits that I do not like as presented.
I don't see why you can't spend enough time, money, and effort to eventually get rid of negative ones or get new positive ones instead but at the same time I take Daryk's point of the process should be both something role played and extensive enough that it could be deemed effectively XP spent in name too. Or else it does become a loophole to get 'free' XP at character creation.
Like I have always said, there is nothing wrong with making the players pay for it, but don't make them pay twice.
IMHO, were AToW truly fails as a system is in the point system trying to do to much, to often, while being to generic.
Don't get me wrong, GURPS one of my favor game system (those its hell on the GM) use a point system. The major difference is that SJGs goes out of their way to insure that every point is balanced vs. each other for character/universe creation. then the system steps back and lets you roleplay from then on out.
For a point system to work you have to put in the effort to make sure the points you spend/get for one trait/skill/attribute/Etc. is balanced with the points you spend/get for another. On top of that you need to separate Character creation points (both mentally and system wise) from advancement in the game. And live with the fact that characters are not going to and should not stay balanced after Character creation. And that what you start with from Character creation is just that, what you start with and you are not entitled to keep it or automatically replace it because you paid for it at the start of the game. And finally, the system needs to have a point range that can both handle the range/types of options without over burdening the GM/PCs with waste points.
AToW fails on all these points.
1. Point cost in the system are not unique and are just set numbers. All trait/skill/attribute/Etc. are treated the same DEX, STR, CHA are all the same Acting, Security Systems, Surgery are all the same in the point system.
2. The point system likes to override Roleplaying as written, yes I know you can ignore this, but as written is does.
3. They system gives GM/PCs this feeling that I paid for its mine till the end.
4. The system also gives the feeling that it punishes players for not "wasting" points on something they got during play.
5. They system point levels are ridiculously high for the sake of being high. As most of the point totals are just 3rd ED points with a zero or two added.
Overall, the system fails to be an effective point based system on all the points that you need for a point based system. What's sad about it is that with a point ranges half to two-thirds as high they could fix most of these issues.
The above needed to be said for my point below.
From the earlier example: the "EM interference" quirk is a -100 XP negative trait, not much in this system. If the player was to replace the PPCs as described earlier, the player would be paying around 500,000 c-bills for the PPCs and what every the going rate for a Mech/tech.
Now if we look into the point system at the trait that covers money for equipment (Wealth) we see that to have that many c-bills is a +800 XP trait. So, at least to me by the Traits as Written if the player has earned the money to pay for this in game, their in-game actions have already surpassed the -100 XP they earned from the negative trait by 700 XP. Why would they then have to pay 100 more XP to get rid of the trait.
This is where again AToWs point system fails due to its unbalanced nature and want to control the in-game balance. Because of the generic nature of points in the system and the complete lack of balance, getting 500,000 c-bill can get rid of a negative trait, but you wind-up have to use 800 XP worth of in-game resources to do it.