You've already played Xenogears so I would suggest Vagrant Story as a good contender, a nice underappreciated gem by Matsuno. I also will give Dew Prism (Threads of Fate) props that what it may lack as a game, its story is actually pretty good. Rue's story is pretty twisted despite the cutesy nature of the game. Brave Fencer Musashi has a good plot as well, its not serious at all but in terms of humor and good characters the game is an absolute treat. I'll have to think a bit more for other titles.