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@Greninjaman
I have my own little perspective on that subject matter myself. Most likely because of the inspiration that I have from the anime - where character development for the Pokémon is pretty important - I almost subconsciously consider Pokémon - in a very general sense - to have a similar level of emotional complexity to humans, or at the very least enough to be considered more than simple animals with only relatively basic feelings and desires. To me, they're not just superpowered pets that will do whatever you say just because you caught it in a Poké Ball or have eight Gym badges... they have feelings, dreams, loves and hates, and philosophies that define them and drive what they do... just like with humans. And while this point is admittedly a highly debatable one if you're more into the game canon vs. the anime one, I think that the more descriptive and narrative nature of fanfic vs. the more mechanical and "blank-slate" nature of the games kind of complicates things a little bit. A reader who's more into the anime canon, for instance, may consider a less definitive approach to characterizing Pokémon à la the games as closer to under-characterization than one that actually reflects what they believe to be the "true nature" of Pokémon (like me writing this post right now, actually... haha). And yet, someone who's more into the game canon may actually agree with that view if they're one to create personalities for their Pokémon or otherwise project traditionally "human" qualities onto them because, again, the games are somewhat of a blank slate when it comes to Pokémon... they could be relatively simple animals just as easily as they could be highly intelligent and complicated creatures.
With all of the above caveats noted, however, I have to say that as someone with a more anime-oriented view on Pokémon, I believe that Pokémon should be considered equal to humans as far as narrative importance goes. Because if we can focus on the emotions and thoughts of the human protagonists, why shouldn't we do the same with those of Pokémon that - Poké-speak and individual species quirks aside - are very arguably similar to them in the ways that matter most in a story? And as characters that are narratively important, it goes without saying that a Pokémon's characterization should reflect that importance, and that it shouldn't be marginalized or oversimplified just because the character in question is a Pokémon.
That said, things can easily get kind of ridiculous if you apply that philosophy too liberally. Consider, for instance, that if you have three main characters and they all have six Pokémon, then that's 18 Pokémon to consider both individual character arcs and roles in the overall plot for, on top of those for their trainers and everyone else in the story! Given the inherent frustration potential in that, I've been thinking - for the sake of sanity if nothing else - that maybe there should be around two or three Pokémon in the party that are "main focus" Pokémon who will have character development and narrative prominence on the same level as the humans that they travel with. The other Pokémon will still matter, of course, but their development will necessarily be rendered in broader strokes compared to the others, or will perhaps be slower and less eventful until a time comes in the story where they can have their "day in the limelight", so to speak, and really come into their own as characters.
Overall:
If you're writing in the anime canon, try to flesh out your Pokémon as much as you reasonably can. Ideally, flesh them out regardless of which canon you're writing in, but realistically, do whatever you feel is most compatible with your own views on Pokémon and - perhaps most importantly - with the story that you're trying to tell.
True. You could also have it depend on the specie. A Caterpie or a Wurmple with the deep complexities of a human is just absurd. >90% just squeaks and acts irritating, nicely dovetailing with the predicable cardboard characters of the anime. And when I say ">90%" I certainly acknowledge exceptions, rare as they are. I would apply a more developed (or should I say evolved) psychological and emotional depth to fully evolved Pokemon (Blastoise, Tyranitar, and of course the mythical ones and legendaries).I agree with you on that. the more chatacters you have, the harder it would be to give each Pokemon character development.
@CrystaI
I've actually been having a dilemma somewhat related to that regarding the protagonist's Pokémon in one of my story ideas. Namely because said story idea takes place in Johto, and most crucially during a time where there were only 251 known Pokémon. Which of course limits the pool of Pokémon available to only Kanto and Johto Pokémon, as opposed to even the expanded pool from the HGSS era, let alone the nearly one thousand Pokémon we have today. Additionally, I want to avoid giving my protagonist the same kind of Pokémon that Ash from the anime had while he was like Johto (including what would have otherwise been obvious choices like Noctowl or one of the Johto starters) as well as the same kind of Pokémon stereotypically associated with the Johto game protagonists (like Donphan or Marill, more obvious choices), which of course limits the pool even further. The current way that I have to somewhat "fix" this potential problem is to simply have the protagonist have three or four Pokémon in his party instead of six, with the narrativeexcusereason being that he would rather spend time raising a few extremely well-raised Pokémon versus six somewhat-well-raised ones. Which is all well and good for battling Gym Leaders and the like... but guess what happens when he reaches the League? Yep, not enough Pokémon for the full battle matchups. Not good!
To adress that problem that problem when the League starts, one idea I've been thinking about was to have the protagonist "borrow" two or three Pokémon from his traveling companions in order to reach the six-Pokémon requirement. There are plenty of opportunities for drama here: because the borrowed Pokémon are not actually his, the level of trust and understanding between him and the borrowed Pokémon is obviously going to be very different compared to the relationship between him and his actual Pokémon, let alone compared to that between the borrowed Pokémon and their actual trainers! And this would likely be true even if the borrowed Pokémon were on friendly terms with the protagonist earlier, outside of the context of battle. There could be potential there to explore the differences in relationship dynamics between a Pokémon and their human friend versus a Pokémon and their human trainer. And of course, there are the more obvious questions like: would a Pokémon listen to a completely new trainer without question just because they're friends, or just because their original trainer told them to do so? And even if they did, how would the relative lack of experience and understanding between the new trainer and their borrowed Pokémon affect their ability to battle and communicate effectively?
Very few people get through one region so it's somewhat unexplored, if you want an honest answer. I would plan on completing a character arc through the course of one region and then deciding whether there's another clear story to tell with them or if you'd be better off finding another character with their own problems.