This thread stated that both Kefka and Sepiroth needs to stay in their pre-evil states. Therefore you have to also assume that this battle also takes place before either one of their respected teams also reaches that point. Then in which case
Cloud wouldn't be very effective since he was getting motion sickness because he wasn't the great SOLDIER that he turns out to be. At best he would be a Shin-Ra soldier, and they weren't particularly effective. Barret would still be a coal miner, with no intentions of running Avalanche. He also wouldn't have a gun grafted onto his arm. Red XIII would most likely either be living a normal, peaceful existence in Cosmo Canyon, or more likely as an experiment for Professor Hojo. Vincent would be in that coffin still, punishing himelf for not stopping the Shin-Ra from the SOLDIER experiments And Sepiroth, though powerful, wouldn't know of his true existence, and thus have no desire to become a god.
And I don't think thre is ever a time when Kefka wasn't evil, but we'll assume you meant before his rise in power. Kefka was well, a pussy. He gained his power through intelligence and subterfuge. When the opportunity came, he seized the Esper's power. Cyan might prove formidible since he was a sentry for Doma castle. Sabin and Edgar probably weren't training to learn to fight the Emperor, or tinkering around with inventions. And Terra was under the Emporer's control.
Really then when we look at things like this... the battle comes down to Sephiroth versus Cyan, Terra, and Kefka. Personally, I think Cyan is the better swordsman, but he needs time to prepare his most devastating attacks, which when you fight Sephiroth, you have no such time. Terra has the potential to be a better magic-user than Sepiroth, but not at the stage of development in which this battle occurs. And Kefka has the better maniacal laugh, but that won't help in this battle.
However, since it's three versus one. I declare ff6 to be the winner. Now if the same teams fought each other at the ending of thier respective games. I'd give it to ff7 easy.