I found some bugs not listed in the OP:
1). When you encounter Giratina in the wild, the game won't let you run away or switch Pokemon. When trying to attack Giratina, the game immediately plays some status related text/animations (it seems to depend on what item you're holding. When I sent out an Arceus holding a Zap plate, it said "Arceus is fast asleep!", and showed the poison animation). After that, it says "Giratina used !" and freezes. Also, when the player sends out a Giratina, the game freezes.
2). When you encounter Shaymin in the wild, the game restarts. Nothing happens when the player sends out Shaymin, though.
3). Upon using transform on a wild Garchomp, my Arceus turned into a badly positioned Gible backsprite with a messed up palette.