Being portable is the only bonus for the GBA version for me. The revised script is nicer in spots but not that amazing. Also, I didn't find the Dragon's Den or Soul Shrine that interesting.
Originally Posted by
Crossblades ^ GBA version. Better translation, music, backgrounds, and fixed bugs. Plus, it has the Dragon's Den dungeon.
I thought the backgrounds were worse as they had to cut some of them out due to the smaller height resolution of the GBA screen.