I'm a fan of the first Baten Kaitos, but it does have a lot of problems. For some (including me), the quirky and unique gameplay mechanics, great soundtrack, and beautiful environments are enough to win them over. For others, the bad voice acting (switching to surround fixes the tin-can quality, but not the actual acting), sluggish and mostly mediocre story, and other issues ruin the experience. Which is understandable. The story does have a pretty good ending that ties things together well though - well, besides one strange bit.
Origins is a big improvement in almost every way. I slightly prefer the first game's music but that's about it, really. Battle system is debatable because they're really completely different, but Origins' is so fast and fluid and fun that having maybe slightly less depth hardly matters. And even the depth part is debatable - deckbuilding is simpler and it's unfortunate that defense cards are mostly useless, but Origins requires a lot of quick thinking and planning. The battle animations are excellent too.
Lots of gameplay improvements outside the battles too - you can use your wings to move faster, upgrade magnus, carry a whole lot more quest magnus at once and do more things with them, and more.
The story, while still a little slow at times on the first disc, is a lot more interesting from the start and not so reliant on a single twist - though it does have some good twists, especially if you've played the first game. In fact, it makes the first game's story a little more interesting in retrospect. And the characters, both playable and NPCs, are much better. Unlike most JRPGs, you only have three playable characters and will have a full party within two hours, which works really well because they're all likable and important and developed. The voice acting and dialogue not only improves on the first game, but is actually one of the best JRPG localizations out there!
Unfortunately it came out a couple of months before the Wii and it both bombed saleswise and got mediocre or worse reviews (and the first game reviewed pretty well) - I think a lot of them never bothered to give it much of a chance in the midst of all the next-gen hype. I know there's not much competition here, but it's the best Gamecube RPG except maybe Paper Mario.