Development time. Coding a battle like Diana's for an MC with an unknown skill configuration would take as much time as an entire episode. And, what if the player had maxed Onyx, who turns out to be largely useless?
Also, the story is on rails, which means battles are guaranteed to be lost or won. If the player has a skill configuration that outclasses an opponent they're meant to lose against, then this breaks immersion. The investment in skills will be meaningless, much like how the stats are already playing out. If you fail a leadership check, nothing changes story-wise.
I think it's said that the MC's magic is more primal and doesn't work in the same way as a mage's. Though, it's not entirely clear what rules this system plays by. It's possible the ability to do fire magic just hasn't awoken in him yet, and it requires a kind of divine intervention.