Jobs, and other character-building elements that allow me more ways to experiment with my party...I feel more "invested" in MY characters as opposed to just moving the game's characters through a story.
Beyond that, level design is really important to me. Levels that are interesting and fun to play through trump simply wandering through generic caves and castles put there to give you something to do. Graphics, music, and the types of monsters that appear all contribute to level design in addition to particular quirks or puzzles that are particular to that setting.
Those are my two biggest factors in how I ultimately feel about a FF game. I love great stories as well, but for me, for this series, it's not as important as the gameplay.