So I had this idea yesterday to add a way to specialize your skill usage in Pathfinder.
The idea is that you are still able to spend skill points on skills as they are now but each skill is also separated into several specializations, based on different uses of the skill (for example acrobatics is divided into Jump, Tumble and Balance)
You can exchange any number of skill points for twice (or if we could find 4 specializations of each skill, 3 specialization points) as many specialization points. Specialization points are then spent as ranks on the individual specializations of any skills.
Specialization ranks stack with skill ranks when using the skill for the specialized action but the max rank is the total of specialization and skill ranks.
If you have specialization ranks in a class skill, you get a +3 bonus to checks on that specialization, like with a normal skill rank. This bonus doesn't stack with the +3 bonus from having a skill rank in that skill.
If your total skill and specialization ranks are at the maximum, you can still spend skill points on that skill, all specialization ranks above max rank must be reassigned to other specializations, which can be in different skills (or can be-combined into skill points at the same exchange rate).
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This would give a little more choice to characters with low skill points, or players who would simply expand their skill use, but don't need all of the abilities that come with a certain skill.
I would make the exchange rate of skill points vs specialization points a little smaller than the rater of skills vs actual available specializations, because i think the added flexibility should still have a price and there should be still an incentive to go with the full skill points.