The thing I run into the most problems with in my TPP fics is absolutely the fact that I made pokémon way too intelligent. You can argue that this is somewhat of a problem for all pokéfic writers that base their works on the human world, as making the creatures mentally above animal level (or sometimes that isn't even needed) brings all kinds of ethical questions to the setting that the fic is not set to be about, and thus have to be handwaved or straight up ignored so that they don't get in the way of the actual story.
Well, what did I do to excuse my human-intelligence mon capable of English or whatever language Kantoans actually speak? By making them actual citizens of the country with full rights, as long as they pass the sapience test to qualify for it. And so in the background of my works, you see independent pokémon walk around on their way to work, pokémon with clothes in their very non-human sizes and shapes, smartphone touchscreens calibrated to different species' touches, special saddle chairs for birds and so on. Humans have mostly given up eating mon with the potential for sapience in favor of vegetarian alternatives or lesser animals like small fish or crustaceans. All hunky dory, right?
Oh wait, except that battling, trainers and pokéballs still exist and have to exist or else the source material and its events completely fall apart.
I luckily haven't explicitly bumped into this problem yet within my stories, but that basically makes the worldbuilding like a house that looks fine and works fine but will collapse the moment you go and adjust the heating. I've been quietly trying to justify the battling system to myself, coming up with some explanations and compromises. The most obvious one is that trainers do not "own" their pokémon, but the mon stays around and battles of their own free will. Trainers become more like coaches and managers. Even teachers and caretakers, actually, if the mon is from feral origins and wants to become a real citizen! Of course it's a bit of a gray area when capturing not-yet-sapient mon that can't really communicate that they don't want to be there or don't know of all the opportunities they could have if they left, but we do need to accept some gray areas for an adaptation of a magical dogfighting game.
What about starters, though? Are we really going to let a kid choose a baby to adopt and raise? No, let's make this more responsible. Let's make starter pokémon be species that need battling to evolve more than some others that simply do it by aging, and let's have the starters be free, sapient mon and old enough to volunteer. Perhaps the equivalent of 10-15 themselves so that they can grow up alongside the kid? This journey could be a kind of partnership program over the course of a summer or something, a learning and growing experience. If the two find that they both enjoy battling and the company of each other, they can continue with the sport - and that's a key word, sport. Boxing has two people beat each other up, but it's still just a sport, and the people are there because they want to be there.
But there's still an awful lot of gray area and potential for abuse here, right? What do we do about that? Well, we could make the world a crapsack hellscape... or we could have people acknowledge this and be moving away from the sport as a society. Protests and social movements from free pokémon and ally humans to outlaw battling or at least pokéballs due to the crimes and mon rights violations they allow humans to do. Only in the past hundred years or so has the real world begun to see minorities gain the rights that they, in our eyes, should always have had. Why couldn't the pokémon world have remnants of more oppressive eras, too?
It's true that this requires some skill to pull off, which might scare people away from taking this route... and there's still the fact that fanfic is really written more for fun or personal expression than to make a statement. It'd be silly to demand tackling of real politics or analogues of it in what's typically an escapist fantasy world - though I'll say it'd also be silly to tell people they can't do it. It's their fic, let them be expressive and exploratory with it. If you don't like it (and it's not alarmingly hateful), just don't read it, it's that simple.
With that said, I'm personally not really interested in exploring these themes deeply in my works despite thinking about the system a lot. I just like having things seem plausible and grounded. It's why the mentions of these topics and systems are pretty brief and surface level in my fics - and, well, also because I don't want to end up stumbling on new problems I need to somehow come up with solutions for. Either way, I'm more interested in the characters of my stories than the world, and so they'll get more of the spotlight.
Okay, that was a lot of writing on a pretty wide problem. Now it's time for one more specific and concrete.
I realized this problem when first starting to revise Seiren was that I'd made Helix die of old age. Now, when looking at the timeline of events, I've said that Helix died for the first time on Mt. Silver when the Godslaying happened (TPP event, second run aka Twitch Plays Pokémon Crystal, big event, over a million arts) and this really messed up Red big time, as he didn't know at the time Helix could reincarnate the way He does, which then leads to the events of HIM and Red becoming the cultist we all know and love[citation needed]. Now, Red's original journey takes place when he's 12 (since it's catchier than 11 and marginally more responsible an age to let your kid wander the region), and that's when Helix is first cloned from the fossil. We also know Crystal takes place 3 years after Red (the game not the guy), making Red 15 when Helix first dies and Him 3 years old before His demise.
However, the prologue of Seiren, where Helix dies again, takes place when Red is 17 and in the rest, he's 18, as there's a timeskip of a few months before the first chapter. With advanced maths, we can determine that this has Helix die at the age of 2-3. Yet He was still kicking it just fine at the age of 3 years back at Mt. Silver before a feraligatr had to go and totally poop the party.
Well, maybe Helix just did better at his first lifetime? Had a better diet and exercise? Yeah, that sounds good. Everything's fixed now, right?
Wrong.
In Seiren, we also have Helix going to school. As consequence of my intelligent mon decision, there is necessary education for free mon just like humans. It's already strange to have several different species learn in the same classroom when who knows how different their rates of maturation and ways of thinking are, but we'll assume they just make it work somehow.
What doesn't work, though, is requiring at least several months long education for a creature that drops dead at 2 or 3. There's very little that they can contribute to the workforce due to their anatomy already, and then the jobs they can do are limited to ones requiring no higher education. Add in the time spent looking for the job, and you should basically have the creature retiring by the time they get into their work life. Well, maybe their physical condition doesn't start to deteriorate at the same point it does in humans' lives? Even then, you're getting like 2 years of work at best. And it's not just this creature - how about all the other species with short life spans? Dragonflies spend only months in their adult form, what does that mean for yanma?
Oh, hold on, Google tells me the ammonite lifespan can be up to 36 years. So having Helix's life be short doesn't even give much of Genius Bonus?
Here we finally spot Mr Occam wiggling his razor at the edge of our sight and we decide to take it. Helix's life span is now not ridiculously short. Bug pokémon either live much longer as well or just don't have the potential for sapience, being stupid icky little crawlies. At the start of Seiren, Helix now dies from an illness rather than old age. Are we good now?
Well... so far, seems like it. And I hope it stays that way.
Wow, I didn't expect to write so much in this post. Thanks for reading if you made it all the way to the end, lol. Maybe you got something out of it and I didn't just ramble for no reason.