Perhaps, a penalty system - if you level something that you haven't been using then more points are needed to advance.
Something like this:
eg.
Gas
.: 1-3 atoms = 1 point (top 3 most used skills)
- Guns (1 atom is needed to gain 1 particle/point)
- Explosives (2)
- Melee (3)
Liquid
.:. 4-6 atoms = 1 point (3 secondary used skills)
- Lock-pick (4)
- Unarmed (5)
- Repair (6)
Solid
::: 7-9 atoms = 1 point (3 least used skills)
- Medicine (7)
- Barter (8)
- Speech (9 atoms are needed to gain 1 particle/point)
Once 'atoms' are installed they form a particle which cannot be unchained.
The order and placement of skills is to be determined by usage, between level and or since the start.
When Level Up is achieved the player is given X amount of 'atoms' (eg. 27), they are distributed and crystallise into a particle within the desired state/layer.
When a skill is used more or less often it rises or falls in the 'atmosphere'. Each skill has correspondingly obvious particle crystalline matrices (size vs state varies - barter gas particles look the same as barter solid accept half the size).
This is an off-the-top-of-my-head concept. it could be made to apply in Fallout (just the penalty concept).
What are the pro's and con's you knowledgeable folk can see in this conceptual method ?