The specialize perk has a very short history of being the only perk to grant a bonus to skill use. It also has a short history of being significantly better than choosing to substitute your perk for a skill point. I might have a solution:
The intention for the specialize perk was always to set someone apart – to make someone a specialist in a particular skill. Granting someone skill points that could legally exceed the level cap seemed to be the way to grant that distinction.
The problem is that the old way 1) broke the “no skill bonuses” rule for perks, 2) eclipses the choice of substituting a skill point for a perk, and 3) still feels over-powered. If the new perk looks like this, is it still a valid choice compared to other perks?
Specialize (skill): Choose a skill. You gain special knowledge of this skill, even if you have no skill points in it. You also may take more skill points in this skill than you have character levels.
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That last Specialize version seems to make a character lag behind by a level, instead of progressing when he takes it. I’m thinking about adding this: “when you use this skill to earn progress, your progress die increases by one die type.”
…which would synergize with Weapon Focus and Armor Training. And allow you to spend your future perks on improving your skill points instead of improving your damage/protection die. It would also act as a Spell Specialization, if you took it with a spell. Now this has potential, without adding to your contests / skill points.