There were two factors that prevented Seiken Densetsu 3 from being localized back in the mid 1990s. According to former Squaresoft employer Fehdrau, the first was that there were glitches in the Japanese version that wouldn't be able to pass Nintendo of America's certification process. According to Retro Gamer Magazine, the second one was that there was a lot of text. Squaresoft (now Square Enix) declared that fixing these issues for a localization would be too costly on a system that late in its life cycle.
There seems to be a planned boss in the place where the party meets Jagan for the first time in Bucca Island that was removed prior to release that can only be accessed by using Action Replay on sample cartridges of the game. The boss's body is submerged under the water and attacks with two tentacles.