I've never been keen on disadvantages giving you points during character generation. It leads to players hunting through lists looking for the overpriced weaknesses, PCs getting a great deal because the GM never remembers to use the weakness, lots of rules lawyering ("Yes, I'm telekinetic ... but I don't have any physical hands...") and/or GMs hammering PCs if they have a different interpretation of the weakness. Done properly it's a lot of work, done badly it distorts the game.
My preference is to use plot points. Weaknesses are worth nothing at time of character generation. Instead, any time a PC's weakness causes trouble for the party the party gets a plot point. Any time the PC's weakness causes trouble specifically for him the player gets a plot point. Plot points can be used to make things turn out better: maybe rerolls, modified rolls, etc.. In particular they can be used to keep PCs alive when the rules would have them die. The GM can also have plot points and use them to cause trouble, that's what happens when the PCs run out but still need one to save them.
Example: In Rick's The Slope campaign the first journey was by the nature of the world dangerous but the GM guaranteed success. In a plot point version the first journey would have been a guaranteed success only because plot points would be used if it looked like failing. The more the GM needed to fudge things the more in debt the party might end up. But if the party prepared well they might end up in surplus and have some points for use later.