The New FFIV

My only concern is how you'll get the script to switch between White and Black, because the game registers, for example Terra and Esper Terra, as the same character, and all the transform command does is switch the sprite set and boost her stats, but the command list stays the same.

The command list doesn't stay the same because morph is replaced with revert. Plus none of Terra's stats are boosted, it's just that the damage calculation routines takes in account the morph status.

Maybe you could reroute the command to make it switch between characters (like say trash locke and replace him with Esper terra, but make him unplayable and his command and stats are rerouted to Terra via the transform command, allowing you to have an alternate command list, stats, and if you wanted, spell list from which you learn from.

While you could change easily Terra's actor number during the fight, it's not as simple as changing "00" to "01" because there might be other thing that we are not aware of, such as when the checks for the actor number are made (magic list loading, stats displaying). Plus it's a huge sacrifice to make a character unusable simply to perform a command list switching. You would need to erase all traces of that character at a story/event level.

Command switching (if morphed) are relatively simple to do if you know a bit of ASM, as shown in this video: http://www.youtube.com/watch?v=x6pXqHXa0Sc