Whoa, someone dared question one of the community's cornerstones! I understand the trepidation, but I guess my response would be this: 1) he's an archetype that is very appealing for a lot of reasons; 2) He is used so damn beautifully in the game.
Magus is cut straight from the Byronic cloth:
http://tvtropes.org/pmwiki/pmwiki.php/Main/ByronicHero And I can see how that gets old, but the archetype is undeniably appealing. I love the almost humorous exaggeratedness of Magus: he doesn't bother to run because
he's too freakin' good for the ground. He's a rockstar, with all the awesome-bordering-on-silliness that entails.
That's why the Byronic hero is appealing -- the sheer
titanicness of him/her. Magus is a human who arrogantly dares to stand up to a force far greater than himself because that force took away something he loved. He is the product of the apex of humanity, Zeal Kingdom, who witnessed its fall and was changed by it, and now he follows no compass but his own. The intensity of the Byronic hero, his "posture" or "stance," is just compelling in and of itself. It's hard to rationalize except to say that it's an archetype for a reason.
I honestly don't see Magus as too remorseful. Judging by Ozzie and his exploits, I feel that the war with Guardia was going on longer than Magus had been in the Middle Ages-- his just gave Ozzie the advantage the Mystics needed to put the humans in a very difficult position. Chrono Cross influenced my view on the war, actually: the humans in that game are portrayed pretty negatively -- to an exaggerated extent-- so I feel like human prejudice must have been behind at least some of the conflict. And Cyrus, well-- I mean, it wasn't murder, really. Cyrus was going to try to kill Magus, wasn't he? Cyrus was surely noble, but in a duel, death is a little different, morally speaking. I see Magus as more of a Chaotic Neutral type. He seems dark and evil because the rest of the characters are very moral, happy-go-lucky types, but he's not really.
That's not to say Magus didn't do repulsive things, and that doesn't mean he doesn't change for the better. We discussed this in the Death Peak and Magus thread, but Magus shows signs of development from the North Cape onward that suggest he actually formed something akin to friendships with the others. In the least, he is the way that the game hammers home the point that you Cannot Do It Alone. As powerful as Magus is, he needs to join forces to win against Lavos.