Just for the record, the most popular manga in Japan is that Pocket Monsters gag manga. PokeSpe apparently doesn't have very impressive sales figures in Japan, either.
Did I ever said it's the most popular in Japan? I said it was the best known in the Pokemon fandom so I mean world wide. Most people in the US and Europe would think about pokemon special when you talk to them about Pokemon manga.
I don't like people talking about the Pokemon characterization in Special Manga where they act like animal for feels like Digimon, whereas Pokemon in the Anime had better characterization because they shown to have more "in-depth" and human-like characteristics which makes it look interesting and more "living".
Firstly, there are a few points I would like to contest:
1) Whatever media that was first introduced would seed the "canon" characterization viewpoint in our head. The very first Pokemon product that came out into the market was the game, not the anime. So, the first original characterization of Pokemon was made to be like the game, a creature that have animal-like instinct but yet contain intelligence that rivals human. Generally they are unable to speak human language, but shown to be able to comprehend human language (but have no further clarification is the Pokemon understand the human language only up to the levels of dog react to the command "Sit!", or fully understand just like how human will comprehend).
Therefore, you can't compare Pokemon like Digimon, because Digimon speaks human language, which consequentially made Digimon to have human characteristics, and developers of Digimon also treat each Digimon as like human characters.
And yet, you can't compare Pokemon like animals in our world, because they have intelligence much higher than ordinary animals. Although they can't speak our language, the Pokemon can still comprehend your word. So they may laugh if you talk jokes to them, they may cry if you tell them a sad story, they may get angry if you insult them, etc. Also, although they still contain animal-like instincts, they also each have their own personalities. Even for the same species of Pokemon, there will be the courageous ones and the timid ones.
So, Pokemon is a kind of character on its own. It is not comparable to Digimon, nor Monster summoned in Yu-gi-oh, also not monster in Monster Hunter, nor animals in our world.
2) Based on the above viewpoint, Pokemon thus then should not treat in the same way as like human characters. What I meant by that is not only in their personalities, but also in their way of actions and reactions and lifestyles towards certain things.
Say for examples, animals do not have intellectual mind-set for the concept of "romance love", they don't attracts to each other because their personalities matches with each other. Animals of different gender were attract to each other only because of chemical reactions with the pheromone of each other. Therefore, there is no flirting and love-chatting in the animal kingdom, where such behaviours and actions were only seeable between humans.
Pokemon are not human characters, although they may have IQ close to human's brain, their livelihood were more close to animals, so one should eliminate those subtle emotions that exist only in human characters, such as mental love interest, shame and dishonour, fear towards religious rules, etc. Also, Pokemon will not have desires that were only for human, such as desire for knowledges, desire for authority/power (do not mean physical battling power in this context), desire for domination, desire for everlasting wealth, etc.
In the anime, the developer put too much effort into making the Pokemon human-like, such as making them dress in human clothing even without the deliberate forcing from the trainer (exception to TR's Meowth), talking to both human and other Pokemon as like speaking a language, make the Pokemon react exactly in the same manner as like human towards certain incidents, even the wild Pokemon tried to solve a problem using the human mind-set. That in the opposite make Pokemon non-Pokemon-like, and unable to pull off as human-character because they are no human from the start. This gives quite an odd feeling whenever I watch the anime, because in the eyes of me as an audience, I never look Pokemon character in the same way as human character, but the developer tried to force Pokemon to be human by giving them too much human characteristics.
If you have so many human-shaped monsters as like in Digimon, I can still accept, but human-shaped Pokemon contribute only a small proportion in the whole dex, so forcing Pokemon to be like human is just awkward.
3) An "in-depth" Pokemon characterization with human-like characteristic =/= better characterization, and it doesn't make a Pokemon more "living" either.
I see many people said Pokemon in anime had a better characterization because... how to say it, independent? The Pokemon were like a character on their own where each had their distinct personality, and you can't see that in Pokemon Special Manga. I will really wanted to argue over that!!!
In Pokemon Special, each Pokemon also had their own personalities. Although it might not be so outspoken and manifestly identifiable as like in the anime, but still each shown to have personalities, which is not just some written data in the middle pages of the book. Their personalities were more clearly seen in situation outside battles.
Say for instance, Red's Pika had quite a naughty and mischievous personality, it can be seen from the scene where it shocks Red when he tried to have a handshake with it in the RGB saga, and it also shocks Bill in the FrLg immediately upon the reunion on SeaGallop. Somehow, you can also tell it from its personal battle style when the time it was not instructed by its trainer. Then, Gold's Polibo can be seen to be quite shy and timid when they time it was still a Poliwag. Crystal's Megaree is very docile and obedient, which is not just hardy as it said in its data. Emerald's Sceptile was then seem to be quite quick-tempered from the scene it used Iron Tail on both Ruby and Sapphire upon the first encounter, and just beat Ruby up for remembering the word said by the boy during the very first time he chose between Mudkip and Treecko. The list can went on and on, you just need to be keen on these subtle incidents to see the natures of the Pokemon.
Well, the Pokemon in the anime show very clearly they each had distinctive personalities, which can be seen very obviously from their behaviours, "conversations" between humans and other Pokemon, action they decided to took and reaction towards certain actions they received. However, their characterization receive the same treatment just like the human characters in the show, which the biggest problem is flanderization. To tell the truth, I can't tell what is the personality of Ash's Pikachu in nowadays, because the characterization of the Pokemon was also fading away just like Ash. The Oshawott in the BW series is then the perfect example of instant flanderization, where its faulty characteristics were exaggerated to almost overwrite its "useful" characteristic in story-development viewpoint.
Flanderization is just so overabundant in the Pokemon anime, where this problem is not only exist in the human characters, but also for Pokemon characters. Therefore, as you see, the way of portraying Pokemon in the anime doesn't guarantee Pokemon to be "better" characterize either. In fact, I just think it rather ruins the Pokemon itself as an animal-like creature but with human IQ.
In the Special Manga, Pokemon's characterization were made to the fine level of "Show, don't Tell". You don't need to tell us what their personalities are, but yet I can see it from the plot itself, and there are background data in the middle to give more informations if you doubt the nature of trainers' Pokemon.
And also, I like the way how Special Manga portray the Pokemon, because it actually matches the original ethic definition of Pokemon as like it was first introduced in the game.
I don't hate how the Pokemon Anime portrays Pokemon (so long as their animal side isn't forgotten) as it can be amusing and entertaining. I'm against it being considered the "right" way of depicting Pokemon as there's more than one way to interpret something and I hate it when Pokemon fans treat aspects of a certain canon as more official than others.