I assume this is going to be for PC. If you do it real time, you need to think of controls. Not everyone is going to have access to a gsme pad of some type, so the controls will have to be reasonable. I would personally like a system wherein you can see the enemies on the normal screen, like they did in XII, but with a more action-fighter control ability (as in Tekken or Mortal Combat or something) rather than the menu based control.
Also, how will you implement things like materia, items, and limit breaks? I have an idea I posted for the materia system here
http://forums.qhimm.com/index.php?topic=7872.0 But anyway, my suggestion for battle would be this:
Pretend you're using a basic PS controller. X, Triangle, Square, O, L1, L2, R1, R2. You set L1, L2, R1, and R2 as skill buttons. You assign spells/summons/enemyskills/commands to one or a combination of those buttons. Then during battle you press the button and woosh. The only problem with this is that it would limit you to only like 15 possible actions, but if you follow my materia idea that should be reasonable.
The main buttons, X, Triangle, Square, and O would be used as basic actions. X could be attack, Square could be defend, O could be Item, Triangle could be jump or something like that.
Items would be fairly simple. Whenever you press O the battle would pause and you could select which item you wish to use. That would "arm" it. Then you press O again to use it.
Now, the only problem with this is as I said earlier, finding reasonable controls that would work for a keyboard. Or I suppose you could just make a gamepad mandatory.
Sorry if this is confusing, I wrote it down as I thought it, so I've probably forgotten something.
Anyway, that's my suggestion.