Pokemon need a second ability slot. One that is based of the physical attributes of a Pokemon and can't be skill swapped.
A unique slot dedicated to the tangible physical traits of a Pokemon.

For stuff like Levitate, Compound Eyes, Disguise, Stinky Hold, Suction Cups, Strong Jaw.

Imagine non-sensical stuff like skill swapping Flame Body to an Ice Pokemon, or how Disguise can't be swamped but Water Bubble can.

Abilities should get a split, like physical and special attack.
With non-physical transferable abilities based of abstract or behavioral concepts.
Stuff like Prankster, Sheer Force, Unaware, Oblivious Analytic, Anger Point, Contrary, Defiant, Klutz.

That would fix Skill Swap or Trace randomly failing on stuff like Zen Mode or Ice Face.