I know you got an answer saying Castform could be a problem, but all you'd need to do is change it's ability in YAPE so it wouldn't change because of the weather. Then you'd just have to change the normal Castform sprite. As for Deoxys, as TB Pro said, all you have to do is change the sprite for the Deoxys of that game. I think it goes like this-
Fire Red- attack form
Leaf Green- defense form
Emerald- speed form
So depending on which Rom you're hacking you'll have to replace a different sprite. (I'm assuming Ruby and Sapphire use the normal form Deoxys sprite).
Sorry for being random, I just wanted to answer and doubted you'd be looking at the thread.