i've played Dark Cloud 2.The cause of the game's current event was due to a bad guy existed 10000 years ago in the past, although he's not the Final Boss.
i've played Rouge Galaxy. The Hero is a decendant of a powerful being who existed 10000 years ago, alongside with the Final Boss.
i've played White Knight Cronicles II. The Hero is one of the main characters who had lived for the past 10000 years, being locked/frozed in an ancient capsule when they were just babies to prevent their growth, until certain people found them. The Final Boss is also a guy supposedly dead, existed 10000 years ago.
and now...Ni No Kuni :). There's a 10000 years ago too.