The GBA version has poorer graphics and sound, and suffers from more slowdowns than the SNES version. Additionally, a scene was censored from the GBA version because of "current events" in Japan around the game's release.
It does however have a bonus dungeon, and let you get an infinite amount of Light Bringer (one of the best swords, known as Illumina in SNES) swords without cheating.
Based on this, you should make up your own mind on which to play first.
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