I still think the original idea behind Eden Legacy handled it best. Unfortunately it was changed because too many people disliked the concept, but the idea was:
Instead of an attack option, you had skills. Each level up, you were given an option of 2 possible skills. Generally, the first skill offered was weaker, but had a more definite hit ratio, whereas the second skill was stronger, but had a high miss rate.
Instead of MP, you had energy. Each time you leveled up, the amount of energy grew. Each skill took off so much energy when used, and if you ran out of energy, you were required to spend one round either using an item or Defending in order to replenish the energy.
This made it so that you had to think carefully about which skill to use, especially if you wanted to end the fight right away. In spite of whatever flaws the game may have, I've yet to see this idea implemented in any other game.