Neither Guile nor Serge is Janus. He's not Guile because the game's director has come right out and said it. And there's actually a pretty decent way to prove that he's not Serge.

It's pretty well established that in Chrono Cross, there are more than just the two dimensions. And, I recall, it's also established that, while not the main timeline, the events of Radical Dreamers do occur in another timeline. And finally, it's established that everybody has one duplicate in each dimension.

So take a look at Radical Dreamers. Magus and Serge, together in the same place at the same time. Pretty much proves they're separate people.