And now we are arguing the religion of...pokemon...OK.
Well, even though Arceus seems to be the 'god' of all Pokémon, that surely does not mean it is the end to the Pokémon franchise. I suspect that they will start to mimic other religions and myth, keep running as far as they can before they die. How much land does a man need?
Grass Guardian has a good point and probably has the strongest argument out of everyone here. And indeed, if they did make Arceus too much like the religious image they were aiming for, people would just go MAD. I personally wouldn't, but I know WAY too many people who would.
And as another note; most of the famous games, movies and books are based in religion. I mean, look at the Chronicles of Narnia, Lord of the Rings and Halo. I can keep the list going but I fear getting off topic. JUST because Pokémon is now starting to mimic Christian faith does NOT mean it's going to end now or soon. It will end, sure, as does everything, but it wont today, or tomorrow, so I don't see why everyone is getting all fussy about this. All you can do is sit back and relax and when it does finally end, just remember all the good times. And just because its going to be old does NOT mean you can't play it over and over again just to enjoy it. Heck, I still play the original Doom games for fun.