I'd like to know, though, how the original "Pocket Monster" came to be identified with Kami? I'd have thought a monster was more of a unique physical manifestation of some grotesque form, rather than a form that represents species of creatures that have some spiritual aspect.
I think three points should be borne in mind here:
1) Shigeru Miyamoto (creator of Zelda, Mario and I think had some influence with designing the first Pokémon games) argues that videogames aren't really works of art - whilst there is inherent artistic value in them, there are more driven by commercial restraints.
2) In explaining his involvement in the Wii game 'Super Mario Galaxy', he says that the best designs are those which are designed with their function at the forefront. Thus enemies in Mario games have very specific looks and actions so that you know precisely how you can defeat them.
3) It's fairly well documented, and someone else has mentioned this already, that the original inspiration for the game was bug-collecting, and the joy you can have exploring and catching them.
Bringing all of these to together, I assume that the first Pokémon that were created were those which resemble animals. As the game design progressed, there was the need for more 'cooler' and more powerful Pokémon which would entice someone to carry on playing the game and catch them (those spawning the first legendary Pokémon).
Not against 'outside' insipiration, the creators of the next games, Gold/Silver, decided to base some of the Pokémon on kami. Most children in Japan know what they are, and there is need to further explain what they are and how thay came about ('oh look, here's a uber-powerful kami Pokémon'), given that kami are an 'accepted' (can't think of a better word) part of the Japanese culture.
This is all (mostly) speculation. But it seems that the original design, based on 'pocket monsters' just evolved and became broader. There is no need to explain where they come from in the games (in a proper manner), simply because the videogames function perfectly fine without them. Having manga and anime based on such a vacuous source is only asking for trouble (although some would argue that as these things are only cash-cows anyway, who cares?)
NOTE: I actually watch the anime. Yes, I'm sad. But it was actually decent during the 'Advanced' seasons...
imho, 'god' is a lousy translation for 'kami'.
kami are more like guardian spirits, rather than a creator/judgemental 'god' who rules all. trying to force the concept of 'kami' through the western all-powerful creator 'god' mold just won't work, if one is looking for any type of accuracy as to what was meant by the concept of something like 'umi no kami' (lugia).
'mom
Is it bad that I only know that because the kami are featured in a M:TG expansion...
I don't really see the current discussion of the role of religion as pertinent here. Sure, it is a factor in explaining why the same explanations in Japan aren't transferred in their original form in the US/elsewhere. But surely it is better to ask, as Zegnarfol did, why the heck religion was involved in the first place? But I suppose if you are going to have uber-powerful creatures toying around with metaphysical abilities, faux-religion is going to feature at some point...
There's a big difference between serious Satanism and the shock-factor punk-rock "Satanism" that teenagers engage in.
It's about the same as the difference between Jesus and Jerry Falwell.
So true (actually, I don't know who Falwell is...) The same can be said about the difference between actual religions and the explanations given for the origins of Pokémon in the games.
EDIT: Now I know who Falwell is, I can agree with the comment whole-heartedly.