Baten Kaitos: Origins is a brilliant game, although I do think you get a lot more out of it if you play through the first game, which is much clunkier and has quite a few flaws.
Skies of Arcadia Legends on Cube is also phenomenal if you never played the DC version. A fantastic cast of characters (and villains!) and an unparalleled sense of adventure. The combat is pretty basic and encounter rate is high, but everything else is wrapped up in such a great package. Flying aboard a massive airship with a recruitable crew is the highlight.
Skies of Arcadia Legends on Cube is also phenomenal if you never played the DC version. A fantastic cast of characters (and villains!) and an unparalleled sense of adventure. The combat is pretty basic and encounter rate is high, but everything else is wrapped up in such a great package. Flying aboard a massive airship with a recruitable crew is the highlight.