Zezyrr said:
It was a game on the PS2, There were two gods, both had avatars that were dragons, a white dragon and a black dragon respectively. You played as a (blue?) haired young male whos (girlfriend?) was the "Chosen" or "Vessel" and was slowly losing her humanity (thus another parallel to ToS in that aspect) you go on a big quest to save her and such. the bosses are dragons of different elements (pretty sure there were fire, water, earth, and air dragon bosses, at least the ones I remember) one of the two boss fights I remember is a water dragon you fight (at the bottom of the sea?) and it stuck in my mind because there was something along the lines of your father being one of the knights who sealed the dragons and he lost his life sealing the water dragon (you get his sword around this point, has a gem set in the pommel which was significant for some reason I can't recall, I think you might get it from beating the dragon) I remember one of the characters you can get in your party is a member of a human sized winged race (they had kinda fairy wings) and he was bad ass you could only get him if you could beat him and he was like 20 levels above any of your other characters at that point (for me he was at least, maybe I just didn't do enough grinding XD) but the other boss I remember was possibly the final boss (not sure cause I never got past him before I had to return the game and PS2) it was the black dragon god and it was intent on taking your girlfriends body as its mortal vessel and you had to go to its realm and fight it or something like that. The ONLY other thing I remember from it was that I THINK it was an Enix game (I seem to recall the logo from any time I started up the game)
I've researched it a bit more, and I am pretty sure you are merging elements of multiple games into one.
Legend of Dragoon: You've got the dragons, a special sword used to seal dragons (Dragon Buster), and a winged race (the Winglies, had fairy-like wings, made of light) and the main character Dart's love interest Shana was the Moon Child, vessel of the God of Destruction.
You fight a Wingly named Lloyd, who is very powerful, but he never joins you, the only Wingly you get in your party is a young girl with a hammer. Dart has brown hair, his father didn't die sealing a water dragon, he vanished after facing the Black Monster. I don't recall anything about a special gem in the pommel of Dragon Buster. Also while there are black and white dragons, they're not gods. The God of Destruction is the Virage Embryo.
Edit: I guess the gem you are recalling could be the Red-Eye Dragoon Spirit?
It's a PSOne game.