This is something that I regard as rather a weakness of the traditional Pokémon game structure – becoming the Champion is basically the end of it.  Obviously you have other sideshows to busy yourself with afterwards, and the games have been getting better and better at those as we’ve moved through the series, but they are, unmistakably, just that – sideshows.  Of course, there’s always the Pokédex project, but I think we can all agree that the Pokédex project is something of a joke at this point.  With the notable exception of Gold and Silver, and the remakes of those games, the storyline is ‘finished’ when the player becomes the Champion.  I think it would be really interesting for a game to explore what powerful trainers can do in the world besides get more and more powerful, as well as the duties and responsibilities of a Champion.

Pokémon trainers are people who work with Pokémon.  That is their skillset; that is their purpose.  It makes sense to me that a powerful trainer with nothing else to do would work on solving Pokémon-related problems for people – or, to look at it another way, solving people-related problems for Pokémon!  Think of it this way: once you become Champion – or, for that matter, after you have been ousted as Champion – you are, effectively, an extremely skilled specialist in human-Pokémon relations with a team of absurdly powerful bodyguards.  Your services should, by all rights, be in very high demand!  A group wants to start a new town halfway down a long, treacherous road to act as a rest stop – but how can they keep things friendly with the wild Pokémon in the area?  There are Pokémon in the ruins that have just been discovered – how can we study the buildings and artefacts without disturbing them?  Wild Pokémon have been attacking a local power plant – what’s going on?  This is all stuff that people might well ask a Champion to check out – or a high-level trainer-for-hire.

Well… what are you asking, exactly?

I think the tacit assumption is that people in the Pokémon world follow a religion similar to Shinto, the traditional Japanese faith.  This makes things difficult for me because I don’t really know a whole lot about Shinto, although from what I can gather it’s much less dogmatic than the Abrahamic religions followed in the West, is built mainly around a generalised reverence for tradition, order and the natural world, and sort of merged with Mahayana Buddhism a few centuries back to create something that’s as much a way of life as it is an organised religion.  Basically, it’s kinda vague and it’s difficult to tell where religion ends and culture begins.  The Pokémon universe is the same kind of thing.  They revere Pokémon, but they don’t ‘worship’ them exactly, which makes it difficult to tell precisely how the nature of their relationship with legendary Pokémon in particular has changed over the centuries.  Clearly no-one worships them as gods anymore, but many of them are still thought of as ‘sacred’ in some sense, perhaps as much because of their connection to the past as anything else (think of the way N plans to gain spiritual authority by reenacting the events of the old Unova legends).  This is further complicated by the fact that many of the original myths, although largely forgotten by the common people, may actually be true – it’s entirely possible, for instance, that Dialga and Palkia really do ‘rule’ time and space in a very meaningful sense.  The people of the Pokémon universe seem to have ‘forgotten’ a lot of their religion, one way or another – they know sites like the Cave of Origin or the Celestic Town ruins were once very important, and still respect them very deeply for that reason, but most of them don’t exactly know why anymore.  Sometimes this can come back to bite them.

I think the vision Arceus shows you in the Sinjoh Ruins is as much an illustration of the scope of Arceus’ power as anything else.  It’s doing something dramatic for you, it’s got your attention, and it wants to show off, so it says to you “this is my kingdom, puny human – the land and the stars, the sea and the sky, your entire civilisation, and all life, from your cells up to the planet itself.  Make a baby Dialga for you?  Piece of cake.”  Your final comment confuses me – by ‘sigil,’ you mean the triangular design that appears where Arceus is standing?  What makes you think there’s something there to ‘crack,’ exactly?

I don’t think there actually is much of a disparity between the games and the anime – obviously the anime depicts them, mostly, as being of human or near-human (or, in a few cases, super-human) intelligence while the games generally do not, but I don’t think the games so much contradict the anime as fail to support it.  You are right, of course, that Pokémon don’t have much of a personality in the games – but wouldn’t we be playing a completely different game if they did?  It’d be a great deal of work to give actual personalities to individual Pokémon, and at the end it would be all but impossible to keep the collecting/training/breeding game structure that’s worked for the franchise since the beginning, so why bother?  And, of course, we still do have Pokémon that are explicitly described in the games as being highly intelligent, such as Alakazam with his ‘IQ of 5000’ (which, incidentally, is an utterly meaningless statement because the IQ scale just plain stops making sense once you get to maybe 190 or 200), or even Pokémon capable of human speech (the ghost of the mother Marowak in Lavender Town).

In short, what I’m suggesting is that Pokémon don’t appear to lack personalities in the games because the games take a dimmer view of their intelligence than the anime does; they appear to lack personalities because the games just don’t care.  When people do talk, in the games, about the intelligence or personalities of Pokémon, they tend to say things along the lines of “just like people!”, and the relationship between humans and Pokémon has always been portrayed as an equal partnership, implying that they are at least of comparable intelligence – quite a bit brighter than a standard cat or dog.

The other thing to bear in mind is that ‘intelligence’ is a frightfully nebulous concept anyway, and that most psychologists would be hard-pressed to pin down what it actually is.  I am actually tempted to suggest that Pokémon are, broadly speaking, quite close to humans (or, in some cases, well above them) in their capacity for logic or ability to guess future events, but fall behind mainly in areas like leadership and creativity, which is what trainers are expected to provide.  But now I’m speculating.