This is a pretty danged good idea, but I'm kind of wondering why you start out with feats but end up with other stuff.
As for balance: I don't know what you're going for (should they end up penalizing overall, or balanced out?), so I can't help there. However, some notes:
Blind is penalizing you more than any other ones, by FAR, consider adjusting.
Energy Specialist benefit is a feat, I think. Energy Specialization? Well, the option is to allow that feat to stack or replace the feat with the flaw (replace the flaw's benefit with the feat).
Ponderous Caster penalty is significantly more severe than everything but Blind. It also makes all Immediate Action spells completely worthless, and almost all Swift Action spell suffer the same fate.
Superstitious is wonky, and I have no idea what it's doing. Is it...you become Shaken, but you get a +2 bonus on the save?
For all of these, I like the idea behind them, but as I said, I can't comment on balance since I'm not sure what they should do. I think most of them offer a slightly more significant penalty than benefit.