I think magica is supposed to represent inner force or spirit, not necessarily magical powers. In martial arts some refer to is as Chi. Stamina represents physical conditioning promoted by, running, heavy lifting, constant drills etc. Magica represents strength of spirit, conviction, and willpower gained by disciplined practice, meditation, meticulous training.
So when my DK swings his blade or blocks with his shield it is a function of his physical endurance and strength. However when he pops dragon scales on his back or channels the strength of dragon blood he is digging into his inner reserves and using mental force of will.
So if I want to play a physical beast, who ran and trained hard, I will put more in stamina and take more stamina skills. If I want to play a more disciplined monk type I will go magica instead. And focus more on those inner powers than on my blade and shield. For me this system makes sense. Boxers have their barrage of punches and Bruce Lee has his 2 inch punch, you decide which one fits your style.