This is one of the few instances where the anime takes a drastically different approach. "Legendary Pokemon" become overpowered, and if they are "used" by a trainer, it's usually a mutual agreenment rather than a clear capture. They're often shown as having some sort of control over the Earth or nature itself, and need to be free to keep that control (Movie 2).
But just because they're powerful does not mean they are God, a god, divine, a deity, etc... regardless of what religion(s) you're using as a basis for a god. They're seen in the anime much as ancient cultures in the real world saw some animals: Ancient cultures worshiped them but modern culture know they're just Pokemon, albeit really powerful with an extent of control over elements.
And there's a difference between a powerful attack and control over elements. A powerful attack is just something that's more than it normally is. It's still confined to where the battle is happening. Just like when "Earthquake" is used but the city doesn't collapse.
But a legendary Pokemon has more power than just an attack. It can control the rain or snow or fire or whatever more than a pokemon using the elements to attack.
In the games, all "Legendary Pokemon" means is "A Pokemon deemed Legendary by Gamefreak." There's no basis that legendary=powerful because flat out, some are quite bad in battles. Many aren't, but some, particularly a few of the birds and the dog trio. Other "rules" such as gender, ability to breed, one-time capture have also been thrown out in subsequent generations.
It's also worth studying Japanese culture and the religions it follows. Christianity and other western religions like Islam and Judaism are the EXTREME minority. I'd be surprised if Gamefreak even employs a single Christian. But parallels between legends and the religion of Shinto could certainly be made.
