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.