Thanks! AU/fusions are so much fun, aren’t they?
I think trainers/shinobi in this world do still have to be highly capable physically. If they are still law enforcement/wildlife rangers/first responders etc. then the trainers themselves have to be strong/fast/smart enough to get to the location to unleash their Pokemon and direct them.
So in the anime, there’s a lot where Fighting-type trainers are often literally training alongside their Pokemon–they both do the same kata / training regiments (if with different sized weights or etc)–and the few human psychics do the same with their Psychic-types if I remember correctly. Even in competitions, coordinators have to be as dolled up as their Pokemon–no slackers in competitions!
I always had a… not a headcanon, but an idea of sorts… that there are probably different kinds of Pokemon battles. Obviously there’s the two-v-two and group battles etc, but I kind of thought–for the less AoE elemental Pokemon that it’d be interesting if there were battles where trainers did actually fight alongside their Pokemon. So it would be Pokemon+trainer versus Pokemon+trainer and not only are the trainers taking the same risk as their Pokemon, there’s a bit of strategy, too, because do you focus on the Pokemon or on the opposing trainer? Do you have your Pokemon protect you? What skills do they have to augment yours? Etc. etc.
So the shinobi-trainers would be a little more active than the anime or game counterparts, but not full out punching Pokemon in the face (then again I’m pretty sure Ash has done that at least once in the anime…) Going with the first responders idea, the people still need to be the one to drive the machinery there and operate the tools or guide the dogs on what to look for etc.
Anyway, so yes. Chuunin Exams would be kind of like Pokeathlon and normal battle tournaments and Naruto canon. Everyone knows that they’re using their Pokemon, but it’s how creative you are or how well trained your Pokemon are is what pushes you over the top.
Like, oh, I don’t know, everyone knows Arcanine are very fast and their flames are very powerful, but can you imagine training an Arcanine to jump and–at the precise moment–emit enough flames to extend their jump so it’s as if they’re flying. A flying Arcanine! Who would expect that? Giant fluffy fire monster just diving down from the sky.
Also, I’m not saying that the AU fusion would be “grittier” than the canon Pokemon world, but there are some instances of actual death in the games so it’s not like brutal death fights to Pokemon battling is necessarily such a huge steps. For the Chuunin Exams (especially the tournament which was open to the public) they would stop at the point of “fainting” but in some of the really bad battles, you know there are some Pokemon and human deaths going on.
… sorry, that’s a morbid point to end on…

Oh, yeah, definitely. It’s a sign of something TERRIBLY WRONG when a trainer’s Pokemon dies. Like… either they’re so inexperienced or incompetent that they cannot discern their Pokemon’s limits OR that trainer is terribly outclassed. Ratata vs Legendary kind of outclassed–one hit kills, kind of thing where no amount of revives/potions/PokeCenter treatments will save them.
It’s why only the shinobi-trainers are licensed to have more than two Pokemon because having a full team of six is so much responsibility and requires so much ability from the trainers themselves. They have to understand each of their team member’s limits, have to be able to make the quick decision to recall or keep them on the field. Know which ones to swap in, which ones to keep in reserve. They’re not allowed to run away, is the thing, so they have to be able to manage their team enough to get the job done without lethal consequences.
That being said, I don’t think the move “Self-Destruct” is actually a Pokemon blowing themselves up so much as it is them essentially releasing the majority of their energy in one huge burst and immediately fainting. They still have the bare minimum to still be alive, but if they aren’t immediately recalled (and healed within a few hours) they do have a very real chance of dying.
