Different strokes, but I really liked the simplification of the battle system.  I found managing every single character's deck in the first Baten Kaitos incredibly tedious, especially as the cards changed over time and you had to keep an eye on them.  The battle system in the first game is also 
incredibly slow and obnoxious at times (though it still has strategic appeal), with the characters calling out every attack at a very deliberate pace and then the game stopping to show the Results screen after every combo.
By contrast, Origins is all about the Speed of Battle, and once you increase your bond with Sagi enough, the game does a pretty consistent job of always tossing you 
just the card you need 
when you need it to continue a combo.  So you set up your hand in-battle for your first character, and very quickly you start developing 
absurd demonstrations of utter ass-kickery like 
THIS.  It's simplified, but it's fast and fun and I'll gladly take more hours of enjoyment from the 
rest of the game over the hours of deck management I had in the first game.
And no one can say with a straight face that the original Baten Kaitos had a good dub, especially if you left the audio settings at their default state so you got that "tin can" audio effect.  Baten Kaitos Origins, though, has an excellent dub, mostly because Nintendo didn't dub it themselves.  And considering the game was a budget title, I always thought the game was quite lovely and the story is 
leaps and bounds better than the first game's (despite the first game having a really well-done plot twist halfway through).
I still liked the original Baten Kaitos for all my gripes with it, but Origins is just a better game with a better story; a more exciting battle system; better characterization; 
much better dubbing; and IMO better music.