You can play through FFCCRof with multiplayer, exactly the same as you can with one player. Also, there are side quests you can play by going to town and eneiring the palace. The field of coop rpg games that are any good is very limited.
A remake of the old stand-up arcade game "Gauntlet" is coming out on the DS later in the Summer, and it is supposed to be great. Not only will it have 4 person wifi multiplayer, but it will also have wifi chat, allowing you to speak verbally to your other party members using the DS microphone or a special headset.