Kingdom Hearts really should have taken a Shonen Manga approach and just had each game be a mostly self contained arc and the next game there is a new bigger and badder guy
Uhh... it does.
KH1 = Sora's first adventure, search for his friends, Ansem as the big bad ("Ansem Arc")
CoM = search for Riku & Mickey continues, introduces Organization XIII, Sora has to get through their scheming, Riku's journey towards the "road to dawn" begins, Marluxia as the big bad ("Castle Oblivion arc")
II = Organization XIII's original plans fail in CoM, they form new ones, Xemnas as the big bad ("Xemnas arc")
BBS = new trio of main characters with their own journeys through the game, Master Xehanort as the big bad ("Master Xehanort" or "Aqua, Terra & Ven" arc)
Days = kind of a "Roxas arc", if you want to label them, not sure if there's a kind of main, main villain, it's more about just Roxas' time at the Organization than fighting a big baddy
ReCoded = okay, so this game is pretty pointless, from a story POV
3D = Sora & Riku's Mark of Mastery Exam arc. A newly recompleted Xehanort as a kind of villain
There's an overlying arc, but that's the case with ALL Shonen Manga. And while yeah, Ansem, Xemnas and Master Xehanort are basically the same being with the same goal, it doesn't change the fact that they've been quite different kind of villains so far.
Kind of your own fault for thinkin 3D would end the Xehanort Saga, as Nomura & everyone has been quite clear that Kingdom Hearts III would be the one to end it all and 3D is the build-up to it.
The KH refresh guide on gamesradar (I think) was over 50 slides for crying out loud
There has been FOUR somewhat major, lengthy JRPGs and a couple of spin-offs prior to 3D. There's bound to be a lot of stuff that has happened & some complexity.