Restricted Cast, who would you pick?

Hmm... that's interesting.  I hadn't considered making ALL of the main characters NPCs.  If you were to do that, then the playable characters could be selected by class, like FF1 (though I'm not sure I'd allow doubles like that game).

If I weren't already working on two other projects, I would be very tempted to make a version of FF6 like that.

I don't know if the commented disassembly is at the point where it has labels and suchlike, and you can delete routines and data structures to free up room; but if it is, you could have the vanilla PCs be NPCs, and develop a smaller set of PCs like in my first post ITT. You can free up a lot of room only needing data for 4 to 6 characters instead of like 15.

Consider also mixing free roaming non-linear events vs linear vanilla FF6 plots (though you can have both, TBH). Having multiple quest systems (message boards, NPCs, bars, random events) would sort of mix them all together, which would be nice but perhaps beyond the capabilities of the game.

Same goes for blank slate characters like TES or Fallout (or Chrono Trigger to a degree) vs games with strongly developed characters who have backgrounds, motivations, and believable writing (what most Final Fantasy games go for and accomplish to varying degrees).

Or you could avoid it altogether by limiting the number of characters you can recruit in a single playthrough, forcing you to recruit the others in NG+ to see their stories.

Or have 2+ scenarios like the SaGa games, where their stat blocks carry over to one degree or another and some characters can only be recruited in specific scenarios either hard-coded as such, or because they were recruited in the previous scenario.

No matter what you do, this post is basically impossible to implement without something that disassembles the event code into abstract scripting language style functions, and the various bytes into nameable variables. It wouldn't be that different from a compiler or assembler, and honestly sounds fun to implement. You could check for errors when the compiled event scripts are larger than the available ROM space, decompile compiled scripts and fart around with them, write code that optimizes the position of field variables based on things peculiar to the scripting language and the assembly architecture.