Tokita had difficulty adjusting to his role as director, particularly as he could not be as hands-on with the graphical elements as he had been for Final Fantasy IV. Except for menus and battles, Fukaya was responsible for all the game's programming. Tokita put an equal amount of effort into each world design. Many of the world suggestions came from other members of staff, with Tokita choosing what he thought were the best. The first world created was the Middle Ages edition, which informed both the wider narrative and the gameplay design. The scenarios originally had a graduating difficulty scale, but Tokita abandoned this so players could tackle the scenarios in any order they wished. Inoue was responsible for the battle system design, wanting to make a strategic experience which Tokita described as "real-time shogi". Another goal was to evolve the standard gameplay of RPGs at the time. One idea of Tokita's that was rejected involved not displaying hit points, but having the character physically act like they had been injured or look weakened as they took damage instead. Once production finished, the team split up to work on other projects within Square.
