Thematically, I really like the idea of a permanent change, the idea that it alters the cannibal when he does this, but it does look like a gamebreaker, so, more tweaking...
Eat The Soul(su)
By eating a murdered victim’s brain you gain a portion of his knowledge and power. If either your victim’s Int or Wis is higher than yours, you gain that score for 24 hours. Otherwise you gain a +2 bonus to either Int or Wis. In addition you may gain one skills, feat, or spell known to your victim. If you roll over your new Int score you retain this knowledge for 24 hours. Otherwise it is forgotten after 1d4 hours. If you choose a skill you gain up to 4 ranks in one skill possessed by the victim in life. If you select a feat you must meet all prerequisites. If you choose a spell you must be able to cast it based on your class and level. If the victim you select suffers from any type of mental condition or illness, such a geas, charm, or insanity, you automatically contract it, whether permanent or temporary.
You must kill the victim yourself by doing the final damage that ends the victim's life and you must devour the victim's brain within one hour, while it is still fresh, to gain any benefits from it.