Yeah... This is one of those problems 'in the box' that really don't come into play. Ever.
But, for the sake of argument, let us say that you have a player who for some reason gets to eat their victims brains. Like some sort of Dahmermage they go about, mixing brain cocktails, swilling it, then adding their champagne to the campaign.
There is no fear of imbalance with permanent bonuses. That's why we have named bonuses. You're giving them an option to have an extra Magic Item... In a mental skill that is less likely to help the user.
If the PrC is made for a Mage the player is going to seek out someone with higher Int... And they're going to find, well, something that is going to be difficult for most to kill unless your Mage is a dullard. Same thing for Cleric and Sorcerers. And there is the problem with the brain.. Why would you allow the character to eat a non-humanoid brain and gain powers? Also, a melee type is going to get what benefit out of any size bump in their mental skills that is commensurate with the benefits of other classes.
+2, +4, +6 based on level for 'brain eating'. The individual can eat 3 brains for their three physical stats. The powers of such sarcomancy is going to be an Enhancement bonus. You're looking at an unslotted item that can be included in the player's share of the treasure, removing the issue of $ imbalance.
The rituals required take 1, 2, and 3 days for each bonus, and the individual cannot have an injured brain. That means no beatings by the party melee specialist, no electrical damage, no criticals... nice, delicious, nutritious brains. No preservation either!
Adding skills? That's a bit easier, but there are going to be limits. Trophies would be good here, and generate some good little objects. The thief's fingerbones made into caps so you 'feel' traps, the eye of a master appraiser. There are rules for skill-boost items out there that cover this
ad nauseum
Feats and spells?
Feats
are the hardest to emulate because there are so many items that grant feats at so many different costs. Alertness will cost you 10k, but Improved Sunder/Critical are +1 bonuses on top of weapons, while Spell Penetration (and a stackable version!) will only cost you 8k?
Spells usable once/day, and you have to be able to cast the thing. Oh, and also you're going to be limited as the original caster would be. So if you're taking that Fireball you best have a 13 Int... Oh, and you also need to be out of your armor to do it, or using an armor that allays that loss of spellcraft proficiency (as the memory comes from the original user it would be trained to that user, so unless they have an Armored Casting ability it doesn't make much sense that you can get away with it).
Yes, you can go about creating a bunch of sarcomantic items. That's alright... Gain all the castings you want, at once/day. But to really take benefit you need to attack someone who can CAST them, maintain the body in a state where it is usable, and be the one to make the kill in a ritualistic way if you're keeping the flavor. Be my guest in capturing, binding, and cutting the Archmage's head open for his spells. But you get one, as a 1/day SLA, bound by the rules of the game. It's not even as good as a regular item, and it's going to cause you some issues.
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Personally I don't like the tone for a PC PrC and think an NPC should be allowed to do as he will. The problems of sarcomancy can be seen in
Mako, the Hellblazer villain with the same shtick. Yeah, killing hedge mages gives you a lot of little stuff, and I'm glad you've filled out your brainbook with a bunch of tricks and tips.. But you're going to want to go after the Big One, and all you really are are a bunch of apprentices Voltron'd together. A better path would be using similar flavoring in the form of a Chameleon PrC that does allow you to get... a bit more into character
.
Now for a villain? Not a horrible idea, and allows you to really go for the gusto. The setbacks aren't needed here, and as someone who doesn't really need to follow the rules of PC creation you have a nice little path to go on. Having a bunch of abilities is only really useful if you're going to be around for more than an adventure, but the abilities you could have... And the grief you could cause...
Slainte,
-Loonook.
EDIT: Also, the idea of farming intelligent monsters... yes, because as we know the cost of intelligent monsters is not too high, given you need to enslave them, have at least two of breeding age, and get them to breed so you can eat their children. Also, a salted brain just doesn't do it for sarcomancy.