Probably the thing the games have in common is the villain; Lavos and Jenova are almost exactly the same in both intent and execution. Giant alien with UBAR 1337 POWARZ falls from the sky a long time ago and begins systematically fucking things up. They infest every corner of the planet, altering lifeforms to suit their whims, and are ultimately stopped by a spiky-haired person with a phallic-symbol sword, though Cloud has to go through a lot more emotional turmoil to do it and still doesn't get a clear resolution, as opposed to Crono who just kind of charges in like Braveheart and starts slashing stuff. Both villains also cause the entire setup allowing the story to take place; without Lavos, humanity never would have arisen, and without Jenova, the SOLDIER program would not have been possible. One of the other common themes running throughout not just these two games, but most of those produced by Square, is that the planet is conscious. The creators of Final Fantasy have stated that all the FF worlds have a Lifestream; it smacks of ancient Japanese religious beliefs.
Sephiroth is quite obviously a Magus clone with silver hair, but unlike Magus, there's not one bit of good left in him. A direct comparison of the two power-wise is difficult because of the lack of cutscenes displaying Magus' offensive capabilities in real terms, so all anyone has to go on in that debate is who they'd rather have on the winning side.
