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.

Well, I would like to note that IVs are permanent and unchanging, so I think they represent, rather, a Pokémon’s genetic makeup and any natural variance in aptitude.  Otherwise, though, yes, that’s more or less where we seem to be at the moment.

So… Pokérus.

Well, they describe it as a virus, which seems very odd since we normally think of viruses as malicious parasites, not as symbiotes, which the Pokérus clearly is – it dramatically improves a Pokémon’s ability to learn and grow.  What this makes me think of is an evolutionary process that seems to have happened (it’s a rather difficult hypothesis to prove, but a lot of biologists like the idea) billions of years ago when the first cells were getting their start.  See, in most plant and animal cells, there are little organelles (cell structures) that we use for breaking down complex chemicals to produce energy; these are called mitochondria.  Plant cells also have another kind called a chloroplast, which is responsible for photosynthesis (storing light energy in complex chemicals so the mitochondria can break them down later).  Anyway, here’s the thing: these structures reproduce on their own, independently of the rest of the cell, using their own DNA (fun fact – although your nuclear DNA is a mixture of your parents’, your mitochondrial DNA is an exact copy of your mother’s, a fact which is extremely useful to evolutionary biologists – look up ‘mitochondrial Eve’ some time).  What this seems to suggest is that they were once completely independent organisms which were somehow swallowed up by larger cells and, instead of being digested or whatever, assimilated themselves into the larger cells and started trading services – energy for shelter.  I think the Pokérus is an example of the same thing in progress.  Give it another fifty million years, and all Pokémon will be born with it.  For now, though, it’s an independent organism, barely capable of surviving on its own, that can insert itself into a Pokémon’s cells and, in exchange for a place to live, can streamline certain aspects of the way a Pokémon’s body functions.  Pokérus can produce exotic hormones that enhance a Pokémon’s awareness and ability to process information and commit it to memory, enhancing its capacity to learn from the battles it fights (hence the doubling of received Effort points).  Perhaps they even enhance a Pokémon’s connection with whatever weird sources of power they drawn on for their attacks.

Hmm… which might mean… hmm.

I think it’s so solid I wrote about it in October.

http://pokemaniacal.tumblr.com/post/34093585438/the-ethics-of-pokemon-training

I think there might have been a discussion about this in the comments to some other question a few months ago… somewhere.  Not sure I remember it all that clearly now.  Hmm.

The eventual conclusion was that stronger Pokéballs are more effective because they are more comfortable for the Pokémon inside them.  I think that being in a Pokéball is a lot like dreaming; their awareness of the world around them is dimmed and their perception of time goes completely out the window, but they can still hear, and they can ‘wake up’ if they realise something is seriously wrong.  Great Balls and Ultra Balls might introduce a mild euphoria into this sensation – a pleasant dream, if you will – so that the Pokémon simply enjoys being inside enough to think twice about a trainer it might otherwise reject.  After all, the trainer has gone to the trouble of buying a more expensive Pokéball, or selecting a more appropriate one.

That does still leave a major difficulty, though: dealing with all the specialised types of Pokéball.  Some are reasonably easy to explain – I imagine that being in a Lure Ball feels like dreaming of swimming, while perhaps being in a Moon Ball feels like being bathed in moonlight.  Others, not so much – some Pokéballs work based on circumstance, like Dusk Balls and Timer Balls, and I have no idea how those would function.  The most troublesome is the Luxury Ball, since the name seems to imply that it is extremely comfortable for Pokémon, and makes them more friendly as a result, but has no effect on how easy they are to capture in the first place.

In short, this is my best guess at how they work, but I am painfully aware that some types of Pokéball simply do not appear to fit the model.

I can’t say I have, but let’s take a look… Go go gadget Google.

You mean this, I imagine?

Hmm.

Yes, I think I would agree with most of that; it makes a great deal of sense.  The theory on apricorns is… interesting, put it that way. I never thought to imagine them as a carnivorous plant that consumed Pokémon as an energy source.  Apricorns and apricorn trees are normally portrayed as entirely benign; I can acknowledge the possibility that they are extremely dangerous to the unwary, but it’s still difficult to swallow (particularly given that Pineco and Beedrill have been shown not merely living in but outright infesting apricorn trees).  It’s a very clever explanation, though.

There are only two other points that I have real trouble accepting.

One is that ‘experience points’ are a real and measurable property of Pokémon distinct from any real world phenomenon; I remain convinced that experience and levels are just abstractions designed to simplify the process of growth and evolution for the purposes of gameplay, and that we’re supposed to imagine Pokémon as getting not stronger exactly but more skillful and more confident.  I am likewise convinced that evolution is prompted by emotional and psychological factors in many (most?) species, and closely tied to that increase in confidence and self-awareness.

The other is that humans are in some sense ‘outsiders’ in the Pokémon world, who evolved in our world and were somehow transported there.  It’s true that humans are generally treated as being fundamentally different to Pokémon in some sense that’s never quite defined, but I think that the general feeling created by the franchise is that humans and Pokémon are ‘supposed’ to be together, that they developed together (granted, this could be a result of human cultural indoctrination, but honestly I’m not yet willing to rule out the possibility that the Pokémon world is the result of a Judaeo-Christian style creation by Arceus).  I don’t think it’s impossible for humans to have evolved in the Pokémon world at all (putting aside the fact that it would be an astonishing coincidence), in spite of their obvious physical defects in comparison to most species of Pokémon; actually, I think that this suggests that the ability to train and command Pokémon came first, followed by superior language ability, upright stance, advanced vision, weaker musculature, and all the other attributes we associate with the evolution of anatomically modern humans.

But that’s just me.  The Cave of Dragonflies version does make a lot of sense.

Y’know, I really don’t know.  It’s anyone’s guess where they’ll go with the next games.  (Incidentally, I think this question has been sitting in my ask box since *before* X and Y were announced).

What I always thought would be enormously fun is to have two or more criminal/enemy factions in the world, like Team Aqua and Team  Magma in Emerald, who have opposed views on the relationship between humans and Pokémon.  Black and White 2 (which I haven’t finished playing yet, so don’t quote me on anything) are doing something like that with Rood and his ex-Team Plasma faction, but the division between ‘good guys’ and ‘bad guys’ is still very clear there.  I thought it would be really interesting to have a group dedicated to shifting the balance between humans and Pokémon, like Team Plasma, in the same storyline with a group dedicated to maintaining and exploiting the current order, like Team Rocket – because a leader like N might be your enemy because of circumstance, but no one would hate a leader like Giovanni more than him… so you have a situation that’s like “who’s the bad guy now?  Why?”

What I’ve always thought is that, in the Pokémon universe, a lot of human words are derived from the sounds Pokémon made – so, originally, humans called something “gloomy” because it reminded them in some way of the Pokémon that makes the sound “gloom”, or name a substance “magma” because it’s where the Pokémon that makes the sound “magmar” lives.  I quite like this idea because it ties in nicely with the implication that the alphabet is originally based on the Unown, and continues to emphasise what a huge cultural debt humans have to Pokémon in that universe… although I have no doubt that certain specific words and Pokémon would still be difficult to interpret according to this model.