It's easy to point out Jeanne D'Arcs flaws. And they're quite major depending on what your value set is. Its difficulty is uneven throughout, the writing is poor (as per usual in Level-5 games) and it really doesn't attempt anything new. However, much of that is overshadowed by the game's amazing presentation (namely the hand-drawn cutscenes), great music and gameplay depth; the amount of customization given is seemingly unlimited and the battles early on require a great deal of planning and thought.
Jeanne D'Arc is a solid SRPG. Being that I prefer that genre to most, lands Level-5's underappreciated effort at number 40 on my list.