What parts of FF6 Advance are modifiable, and how easy is each part to modify? Specifically:
How easy it is largely depends on the code you have to tweak in most cases. But since I have no experience with ARM/THUMB (whichever FF6A uses, I don't know) I can gauge it based on the 65816 instead:
1. Formulas. Say, removing level from all formulas, so only stats (like Strength, Magic,...), equipment, and abilities are considered.
Relatively easy, as both damage formulas are well-documented.
2. Remove levels, but keep experience and level ups. So, it takes (n) experience to level up, and you can level up indefinitely.
Unless you had some kind of algorithm system to keep track of progressive experience, I imagine this would be somewhat difficult.
3. Allow negative stat bonuses for Espers.
Easy. I believe the esper bonuses are well-documented as well.
4. Expand the number of spells available on each Esper.
Semi-difficult, as this involves expanding (and moving) the esper data to allow for more spells, then changing the code involved to check for those spells as well.
5. Make Espers function like Materia in FF7, but with no leveling up. That is, when you equip an Esper, all it's spells are usable, but you can't learn them.
I don't think this sounds that hard to do, but tweaking the code that checks for magic learned at battle init may be tricky. But then again, probably not.
6. Attach commands besides Magic to Espers.
Very difficult, and this goes beyond expanding the esper data. The there's 255 spells which is what that data checks for by default, and there's no way for it to know if it's a command or not. After you deal with that, you have to tweak a bunch of code in C1/C2 to check for those commands in the magic menu, too. That will be far more difficult.
7. Allow two Espers to be equipped.
You have to find 1 free byte of SRAM per character, and there's 12 characters that can equip espers. After you find that, changing the relevant code in C3 should be easy enough, as long as you know what to look for.
8. Change what several of the stats do.
Difficult, as you have to change the "Equipment check function" as it's been called. Basically, one master routine is called for all current party members to update their stats based on their equipment. It's a pretty big routine, and I imagine a bit of a beast to keep track of. It is well-documented, which could work in your favor though.