Well, I always considered FFVII a lesser game to CT, so I would most surely hold Magus in higher esteem than Sephiroth. Now, I know full well that's a bias of nostalgia speaking (having played Trigger far earlier), but oh well.
Not to say that Sephiroth isn't neat but... I thought they truly messed up in how they used him in the game. He seemed far too impersonal and distant for the majority of the time to give much of an impact, and only in the flashbacks did he come into the fore. Magus, too, was in the distance for a while, but he came to quick prominance when they found him. He begins as a shadow of history, a menacing figure of the past and then, unexpectedly, becomes personally pertinant to the present. Had Sephiroth actually come forward and spoken, exchanged insults, or anything, rather than just striking down Cloud's allies in silence, his character would have been far better served. As such, I usually see Sephiroth as a character of great potential, but rather ill-used. Even in what I saw of Advent Children (and the bits I saw didn't really make me like it - here for once I must say I think I would even have preferred the Japanese voice acting to the English), he was nothing more than a phantom menace brought in for appearances.
Janus, on the other hand, is truly central and strong to the story. Though Lavos is the primary threat, the majority of the tale revolves around the royal family of Zeal, particularly Schala and, as an extention of that, Janus. What it seems to me is that, though many time-periods are involved, the primary conflict is the ancient human royal house of Zeal - the mightiest family in history - facing off against the Infamous Immortal. Basically, the best of humanity (personified mostly in Janus), against the best of the enemy. Moreover, by Kato's own explanation, Janus, if not in his guise of the Sorcerer then surely thereafter, is a hero of sorts. He's said to be noble. He might be nobility that's fallen from grace, but he's so bloody strong - physically, magically, and mentally. He is not insane by any measure. A little bitter but, looking at his demeanour in Radical Dreamers, as well as Guile's in CC (which parallels Magil's; though he is not Janus, I think it might be assumed that his character traits are similar, and Guile is what Janus would eventually have become in action), he is a true and proud aristocrat, cunning and of sound mind, sure and determined. He doesn't have that Hitleresque megalomania that Sephiroth possesses (to borrow what Hadriel said); he has a reasonable, if somewhat vengeful, purpose which, ironically, is for the salvation of the world. And, when such things as drove him to violent deeds are removed, he can switch out of the warlord tyrant persona at will. Essentially, ill-fortune cannot destroy him. As a person, he is dauntless and invincible. The same could not be said for Sephiroth, who is essentially a powerful general-figure driven to madness.
So that's why it's Janus over Sephiroth every time. Oh, and I figure that Janus is physically stronger, as magically adept, but more mentally sound. Who would win? It's quite plain. I think Janus could keep his cool far better than Sephiroth. And, from a storytelling/character standpoint, Janus has the far more interesting and complex saga.
