Think about Tina from FFVI, who has blond hair in CG but blue hair in game.
Terra?
http://www.youtube.com/watch?v=eIHy8Q-Z6HETerra has green hair in cg and game. Celes has blond hair and has moments where she looks alot like Terra.
I think in regard to Magus, he probably fell prey to the same thing that happened to Breath of Fire 3, art gets advertised on one channel, and sprites are based off a different and sometimes changes are made without everyone getting told. Or the team changed some colors for esthetics. Colors and appearances are pretty important, and I'd say that the switch to purple was a contrasting change to his appearance alterations. My guess is they didn't want first time players to know that Janus is Magus, while the purple cloak, which signifies royalty, still hints at it. Additionally, his haggard appearance is either a ruse, (In Rd he doesn't have so rough an appearance) or its designed to demonstrate the 'darkness he survived' in his vengeance against Lavos.
As far as being cool goes, I'd say one of the interesting things he has going for him is he has the traits to be a protagonist, even an anti-hero, and yet he isn't
the main character. He's a story element, but its not his story, which I think in turn places a different emphasis on how players perceive him. I'd say its a similar element utilized by Auron has in FFX
