Apparently I can't decide on how to pronounce Arceus, since I use all three pronunciations (Ar-key-us, Ar-say-us, Ar-see-us) interchangeably. I also have really no idea on how to pronounce Kyogre because of its spelling (I used to say key-ogre, recently it's been ky-ogre), so I've been using the Japanese name Kaiorga instead.
Also, I can't stand the anime's pronunciation of Reshiram (ram with a long A sound), and ever since I learned what its name was, I've been calling it Reshiram (ram with a long A sound) instead. When I was a kid, I pronounced Nidoran as nye-dough-ran. xD I also had the Illumize thing with Illumise's name.
I also say Cryogonal as cry-og-gon-ul.