Dargor,
I thought of a few more random but important things you might need to implement if you want to be able to completely duplicate FFVI:
1) Music: The music needs to be able to play both on and off endless loop, but that can also allow story events to alter these loops. Otherwise, there is no way to re-create "Dancing Mad." While on the topic of music, MP3 support would be excellent. As formats themselves tend not to have endless loop options, the best way would be to probably create at least two markers in the SDK for each imported song: one to mark where the song loops, and one to mark from where it loops near the beginning (if the song has an intro, that will likely be omitted in the looping procedure). Dancing Mad will clearly need more than two loops, each of which again must be able to be altered by story events.
2) Serpent Trench: Part of this involves moving automatically in Mode 7 and being able to choose a left or right path within a few seconds, while fighting battles every so often. It seems that these battles are planned rather than random, so the ability to place random battles here would be nice. Also, it would be cool if the Serpent Trench could be engineered so that choosing left or right paths during the trench also altered where you end up when the trench run is complete. (For example, perhaps if you choose left, left, you end up in Nikeah, but if you choose right, right, you end up in a different town.) Finally, it would be nice if the trench can be extended so you can choose your path more than twice, and if you can have more than one trench-like area in the game.
3) Title screen stuff: Here, I'm wondering about the special effect that the game title makes when it rises during the title screen. I don't know if this is done with sprites or if it's a 3D effect. While talking about the title screen, the ability to recreate the Mode 7 Magitek march to Narshe will be interesting, especially since the SDK should allow for the altering of the map, the snow effects, the length of the march, and precisely when the town seems to get closer. With all the Mode 7 stuff in the game that should become alterable, it might make sense to create a Mode 7 sequence editor.
4) Equipment: Temporary characters sometimes have equipment that cannot be removed. It might be nice to have a checkbox for each character's starting weapon, armor, or relic that cannot be removed. It would be nice to change this option with story events as well.
5) Random Battles in the Air: I'm not sure how Doom Gaze/Death Gaze was implemented, but it's another interesting exception to the way the game functions normally.
I'll keep thinking about other things you might not have considered and I'll let you know once I have more.
-- Clockwork Butterfly