That, and the blaringly obvious error that grass- and fire-type STAB moves (or it could be certain Pokemon using STAB, I haven't ascertained yet) cause the game to crash in no$, which I prefer because it can emulate at about twice the speed of VBA.
Around the time you came out with this, I was already working with it in the same way (comparing the Japanese Touhoumon Renkou version and an unpatched Japanese rom), so I may try that again (or take a closer look at what you've taken note of). If I find anything, I will post it here, but you've done pretty much as much as I expected to be able to (get a buggy version working).
To document what I've tested in no$gba:
-Using a fire-type move with charmander causes a crash. Normal has no such effect
-Using grass-type move with Bulbasaur crashes; Normal and fire have no effect
-Using water-type move with Lapras and psychic-type move with Hypno has no effect
So obviously there are some types I haven't checked, and it's possible that it's just Pokemon up to a certain point in the dex.