[Gene Yuss]

Wikipedia has a whole thing on this:

Spoiler:

* The similarities between the world map of Sylvarant and Tethe'alla in Symphonia, and the world map of Aselia in Phantasia.
* The name of the world in Phantasia, Aselia, and the name of Lloyd's hometown, Iselia.
* What's more, in the end of Symphonia, Lloyd leaves Kratos's sword, the Flamberge, by Anna's grave. In Phantasia, the Sorcerer's Ring is found in an underground temple near where the Flamberge is in that game. The Sorcerer's Ring in Symphonia likely was returned to the Temple of Martel, near Anna's grave as well.
* The names of the moons in Phantasia, Sylvarant and Tethe'alla. These names are the same as those given to the worlds in Symphonia. Further, Sylvarant's moon in Symphonia is called "Tethe'alla," meaning the inverse is possible, if not likely. This would mean that the recombined world would have two moons, bearing the names of the two worlds, as in Phantasia.
* One of Lloyd's final weapons, the 'Material Blade,' are two of the three components necessary to forge the Eternal Sword in Phantasia, the Flamberge and Vorpal Sword.
* Cless's fighting style is a fusion of Lloyd's (various techniques like Sword Rain), Kratos's (techniques like Hell Pyre), and Regal's (the inclusion of Swallow Kick). In a skit in Symphonia, Lloyd mentions he would like to learn how to fight like Regal, to which Regal accepts.
* The possibility that Suzu Fujibayashi in Phantasia is a distant descendant of Sheena Fujibayashi in Symphonia.
* The existence of Ymir Forest as home of the Elves in both games.
* The fact that the final enemy in Phantasia, Dhaos, has angel wings in his final form; just as the 'angels' of Cruxis do in Symphonia and that the energy comes from Derris Kharlan.
* The renaming of the Great Kharlan Tree in the finale of Symphonia, where it is implied that Lloyd renamed the tree Yggdrasill in honor of the fallen hero/villain, Mithos.
* The similarity of the names of the heroes - Lloyd's "Irving" is very similar to Cless/Cress's "Alvein," given that Japanese pronunciation does not differentiate between the letters "r" and "l," giving "Arvein." It's possible that the name "Alvein" was an attempt at translating the English name "Irving" into the Japanese character system, a translation later done differently with Lloyd's "Āvingu."
* The existence of Martel in Phantasia, as well as the other summon spirits, save Celsius
* The location of the summon spirit Origin, who appears in a forest behind the home of the Elves in the Ymir forest in both games.
* The book Abyssion uses is called the "Necronomicon" which is also the name of Klarth's book/weapon he starts with in Phantasia (even though the book was destroyed by Genis after the battle with Abyssion).
* Similar themes concerning discrimination of half-elves.
* The angel Dhaos is from Derris-Kharlan, home of angels in Symphonia.
* The mention of the long-dead legendary pirate, Ifreed, in Phantasia and the presence of the pirate Aifread in Symphonia.
* In the anime adaptation of Tales of Phantasia it is stated that Dhaos returned to Derris-Kharlan.