Rayquaza's Motives
A common complaint about the Subspace Emissary is how Rayquaza's portrayal is so strange compared to how it's depicted in the Pokemon video games, such as its hair-trigger temper, and the fact that it seemingly resides in a lake.
I think there's a good reason for this, it's just that it wasn't properly shown in the game.
Rayquaza wasn't living in the lake, it was knocked out of the sky by Fox's crashing Arwing. This would explain why the first thing it does after emerging is attack the already-crashed vehicle. Then, it proceeded to attack Diddy, because it either assumed Diddy was responsible, or it was simply ticked off beyond reason.
