Hmm...
I like the idea of breaking a mob's immunities with an SC. Obviously, Scission should be a more potent Earth reduction than than Gravitation (1/2 that) or Darkness (1/4), as it could be considered a utility exchange for potential damage. Put simply, a mob immune to Slow could be inflicted by it (100% if Scission induced, 1/2 or 1/4 otherwise) while maybe a neutral mob could get an even greater Slow effect landed.
Another idea, as others have stated, is tying some kind of debuff to the SC. Impaction could hamper enemy crit rate while Detonation fiddles with its evasion. So on and so forth. What could perhaps apply to both of this, in regards to imbalanced TP gain, is the amount of each TP used in each step of the WS could be documented and combined to further modify the overall potency of the effect.
Otherwise, mobs reacting differently to various SCs is kind of a no-brainer in concept. Undead should probably hate Transfixion/Fusion/Light, so it could mean further bonuses to damage or effects. Much like we have Abyssea's current weakness system, SCs could get an equivalent that'd boost a mob's drop rate or something beneficial.
Just keeping it limited to MACC seems kind of lame, though.