DS version is my choice, the revamped script (just slightly better than the GBA) new story sequences that fill up plot holes, better localization (Feymarsh just sounds cooler and more mystique than "Land of Summoned Beasts"). The Augment system combined with the revamping of a few character (OMG! Edge and Edward are overwhelmingly useful!
) made the GBA's switching party members by end game a moot point. The revamped difficulty makes the two optional dungeon from the GBA version a moot point as well. Plus, the GBA lacks the rather fun and amusing Whyt mini games that seriously break up the monotony this game has.
I also love the new feature that allows you to read your parties thoughts while in the menu screen. I felt it fleshed out the characters better and overall its a feature that should see future use in the genre.