Plus, this was one of the first games EVER to let you play as a boss you fought earlier in the game. That's what made him so alluring to me.
I agree. The only game I've played that let you do that prior to CT didn't give the characters a personality. If not for that twist, Magus wouldn't be anywhere near as cool as he is; he'd just be a particularly stubborn villain with a tragic past and a record of unbroken failure at all his schemes.
Changing the topic a bit, am I the only one who sees a proto-Magus in Necrosaro (Dragon Warrior IV)? Pretty badass, tragic story, involved in the plot, and after a certain revelation at the very end of the game I wanted to turn him into an ally. The remake *spoiler spoiler*. Much better than Golbez, who appeared the following year.