It would give you a lot fewer options, and that's basically what you have to do to make things harder, give yourself fewer options.
Other possibilities: No item world (except when the game requires) No repeating maps, you only get to use item world (can then add "and then can't use the leveled items" onto that) Use only monsters (unless throwing is mandatory, I can't recall if it ever is) Use only a single weapon type
Those are the tamer ones I can think of, off the top of my head.
This guy is not what he pretends to be. He's the Devil.
Permi-death. If a character ever dies, you either have to delete them or put them in detention. If Mao dies, you have to restart either the entire game, or from your last save. No restarting to avoid another character's death.
Using only story characters and using only the abilities that they have; you cannot learn a single ability (eg. Heal, Fire, Wind, Ice, Star etc.). You can also think of using only one character on the map at a given time and level using only the IW world with no help of specialists. Many ways to make a game harder.