That's perhaps not the best example of where I was going. How about a 'Bad Eyesight' background that significantly hinders searches and ranged attacks, but you get a bonus to hearing checks? Or a 'Weak Health' or 'Body Odor' disadvantage?
As long as the disadvantage is a definite disadvantage, and not "+ a bunch to something you're going to use on this character, but - 50 to Lockpickery." Then, you just go "LOLZ! That character wasn't ever going to pick locks, anyway. I JUST GOT A FREE BONUS!"
I think that kind of goes along with their goal for stats. That way, you could actually have things like that. If your eyesight legitimately affected a definite frequently-checked factor, then bad eyesight would be a great balance to some chosen bonus.
Another example would be "You do less damage, in general, but you inherently ignore 5DT worth of armor." Now, you can build that character to be a better armor-piercing character. BUT, you have to have a large enough portion of enemies in the game actually have 5 DT or more, and you can't have that character do so little damage that they can't hurt anything and are ONLY viable if all they ever fight are armored foes, etc.
It's kinda hard to pick those tradeoffs, but a lot of that just relies on general game balance. Which is why it's best to kind of balance your core factors, if you can (enemies with high HP, damage values, typical armor values, bonus values, etc. -- get 'em all centered around some kind of nucleus), instead of just trying to balance this one thing against that other thing, succeeding, then trying to balance THOSE things against some other thing...
Still, it's a bit of a puzzle.