But since we both agree that the SNES and GBA versions are different enough to warrent seperate runs there's no need to debate it much further. ;)
How well do you think you'll be able to manipulate Zeromus's actions? I haven't checked, yet, to see if Big Bang's damage was lowered by stealing the Dark Matter yet, I've only fought him once so far. It's possible that's another 'bug' that was fixed, though I always thought the Dark Matter theft was intentional.
There's actually a discussion going on in the Final Fantasy III topic about whether Locke's scenario should be skipped entirely due to a new glitch found that lets you walk through NPCs. You may think that's stupid as well, (and I personally would much rather see that part of the game done, too), but it's very personal what people think of it.
At any rate, due to the differences, I still think a seperate run of the US FF2, or JP FF4 on the SNES should be attempted by someone, if only for exploiting the greater number of glitches left in it.
I should note that according to my testing the Warp glitch in the Dwarves castle crystal room no longer works in the GBA version. This will force you to do the sealed cavern later on and will add quite a bit of time that could have been avoided otherwise.
On top of that, both leveling tricks in the Tower of Babel no longer work. Searchers now summon Centaurions (which give far less EXP) instead of D.Machines - heck, I haven't even seen D.Machines or whatever they're renamed to in FF4 Advance yet - and the Attack/Defense Nodes of the CPU no longer give experience.
Back when it was just Blip's/Phil's patches, I noticed that FCEU would lose its hotkey settings if I loaded one of the older, "official" versions of FCEU. Though sometimes it would lose some of its hotkeys anyway... Is that related to this?