Here is an idea that is somewhat farfetched:
Janus: One among you will shortly perish.
Janus predicted the death of Crono.
Serge "predicted" his murdering of Kid.
You must be joking. Premonitions are hardly a unique circumstance! True, Serge has some foresight, as does the child-prince Janus, but the ability to read and feel omens being a commonality is hardly grounds for them being the same.
Can this theory not simply die once disproven? The fact of the matter is simply this: Serge looks different, thus his bone structure and DNA is inherently different. On the physical side, they are surely not the same. Likewise, mentally: Janus is swift to angry speech, Serge is silent and compassionate. The only caring Janus shows is for his sister, whereas Serge cares for everyone in his group and, indeed, if the path goes differently, spurns her company upon first meeting. If he was truly Janus, and had any trace of such a mindset, that is not a very caring or brotherly way to act, considering they had been seperated by millennia. Thus their emotions differ as well. So what then remains? The soul? Perhaps, but nothing can be proven either way for, if the soul does not make its presence apparent, neither then would it have any influence on their caring for Schala, thus it may be discounted.
So there we have it, and I hope finally. Even if Serge WERE Janus, he is so changed that he is inherently a different person, and his caring for Schala is no different than that which any other would give to her, had they known her as well as he did. In fact, his love of her is far more amorous, and if he is truly her brother, that would be a strange thing. If Serge is Janus, Janus is dead. But to even assume this, one must raise only the loosest connections possible. And are we not forgetting Guile in this? Yes, there was an intent for someone to be Janus: Guile. Why then would they, if they lacked the time to tell his story, covertly mean another to be Janus? It is quite the absurd stretch.
It's as simple as that.