Baten Kaitos Origins continues the theme of its predecessor -- that is to say, giving the player expressly indirect control over the proceedings. The player isn't controlling Sagi so much as they are guiding him. Sagi will consult the user for advice, and many characters (those who are consciously aware of spirit guides) will refer to players directly.
A consequence of this mechanism is that the only level of customization comes in the form of interface and the name of the spirit guide him/herself. None of the other characters can be renamed.
Origins refines Eternal Wings and the Lost Ocean's card-based combat structure, now allowing characters to have a shared deck of cards. In addition, the new combat system is faster-paced, and slightly less forgiving.