Each main city and continent have their own theme and mythos(both fictional and homages to the real world) significance within the game. That isn't anything new as writers time and time again use the past to inspire them.
And god forbid that those whacky Japanese take anything from their past and incorporate it in anything you have to buy.
Yeah, I'm not sure if this is lazy writing. I mean, most of the names of familiars, suggested names after catching them, places, NPCs, quests, etc. are all basically play on words scenarios of existing phrases and tropes. None of them are terribly "original" if you will but I've often found myself being like "Oh, that's clever" when a new name or character is presented. Puss in Boats/Bouts is a great example.
e.g. Kublai Khan. That's not a reference, it's just a nametag which doesn't make sense in the context.
Well there is a direct link between Kublai Khan and Xanadu. There is essentially no trace of the city besides writings by Marco Polo and one of the main myths he writes about is Khan's relationship to dragons. He writes about how Khan's chariots are pulled by dragons.
Khan in the game has dragons. Maybe it's not as great as changing the name a little bit, sure maybe I'll give you that, but it's not completely without reference. Keep in mind as well, the events that take place in Ding Dong Dell are almost verbatim what happens in the nursery rhyme. This whole game is footnoted.