Of all the JRPGs I´ve ever played, Xenogears has the best story.It´s very convoluted, and I had to look for explanation on the net, in order to try and understand it.
It´s quite complex and deep, plus it´s one of the best games I played on the PS1, a reminder of how good Square was in the 90s.
I felt Xeonogears overconvolution is what made the story not so good. I played 40hrs into the game, with no discernable plot in site. It felt like most of the game was Fae aimlessly wandering from town to town being swept into situations that are not all that connected. Was not a fan of that. Fortunately the battle system was superb.
My personal choice is a no brainer, FFVII. I enjoyed the characters and themes. I always appreciate an RPG that does not exposite to you (FFXIII) but lays down the necessities to get you by and then lets you discover the details on your own. Most JRPGs of today no longer do this, which is sad. That was part of the enjoyment of traveling a world map. You never knew what mystery you could uncover. Example, Vincent being a secret character. He also has a cave tied to his story that gives you insight into Lucrecia and Sephiroth orgin. None of it is required, but when you do it it enriches the story as a whole.
I very much enjoyed PS4's story. Yet I cannot say if it is the Story I enjoy so much, or the enriched Characterizations of the characters. The series definitely takes the medal for individual Character growths.
Kingdom Hearts series has my favorite light hearted storyline, with a mix of a convoluted epic. KH dips into tropes I hated in games like Xeonogears/saga but maintains a certain level of consistancy in pacing that they lacked.