The World Government actually wants to keep Vegapunk as far away from Pokeballs as possible, for certain reasons.
The fact that trainers have to yell out exactly what they want their Pokemon to do does create a tactical disadvantage, and it's something that the Pokemon and Pokemon trainers in the story will need to overcome in order to remain relevant in the face of the progressively stronger One Piece characters, though there are workarounds in the same way that Observation Haki has workarounds. No matter what happens, though, the trainers themselves will at no point become redundant and they and their Pokemon will always be a package deal when it comes to major fights.
As Zoro's fight showed, Pokemon also have a lot of natural resilience that ordinary fighters don't, which is one of the big things they have going for them on top of the special effects of some of their moves.
Next complaint is not real feel free to ignore it. Why no rhyhorn? Rhyhorn gets no love if it's not a Brock fic
If the Straw Hats had a Rhyhorn on their team, it would either have Lightning Rod and make Skypiea laughably easy, or it wouldn't have Lightning Rod and Spruce would kick himself so hard he would die and the story would end. Had to be done, unfortunately.
I view Sanji's treatment of Nickel as being somewhat similar to how Luffy spares his enemies. Not strictly out of mercy, but because what he did was actually the crueller option. Ordinarily, Sanji would have just kicked Nickel into oblivion, but because he was in that specific scenario with the soup already there, he chose to take the path that would inflict the much more grievous damage.
Sorry to hear that Copper's gimmick falls flat. The sneezing is supposed to be because he's a poison type trainer, and sickness is close enough to poison type vibes. If it's any comfort, he's the only member of Team Steel's leadership that I currently have no plans to revisit in the future.
I would commit unspeakable acts to be able to write this story's chapters within a day.
It'll take a while for the story to get there, but yeah. Ghost types on Thriller Bark wasn't even a question.
Aura and Haki aren't necessarily the same thing. They're closely related to each other, and Observation Haki is almost identical, but there are some key differences that will become more apparent once the Straw Hats start using Haki themselves and Spruce becomes more proficient with Aura.
If I tried to give everyone a full team of six Pokemon I would be crushed by my own hubris. It won't just be Spruce who gets a full party, but most of the Straw Hats are just going to get the one main partner Pokemon. The Straw Hats who are already strong enough on their own don't have much incentive to incorporate Pokemon into how they fight, whereas the weaker ones like Nami and Usopp will be more pushed into becoming proper Pokemon trainers. Even then, there are almost no scenarios in which one of the main Pokemon battlers is going to have a full team of six Pokemon all out in a battle at once.
Left it out of the quote but your speculations surrounding which Pokemon each Straw Hat might acquire were interesting, and there were some that I hadn't even considered. The lack of Vivi wounded me deeply.
Not every member of the crew will be leaving IronIsland with a Pokemon, especially because at this point that would mean having half the crew go off after the main battle is finished and have some kind of meaningful encounter. It would feel too rushed at that point, and I don't want every Straw Hat to suddenly have a Pokemon each after just one island. That would be a nightmare with balancing Little Garden and Drum, and spacing it out adds to the sense of progression, I feel.
Some notes:
-The Ralts suggestion brings to mind an image of Luffy with a Gardevoir that throws a black hole at Blackbeard in some big showdown (possibly Impel Down?) and I found that funny.
-Hancock getting jealous over a fish is funny enough that I am considering changing my plans for Luffy to incorporate it. I also imagine that he would try and jump into the water in order to try and play with it and be in constant need of saving.
-Sanji suffers enough post-Thriller Bark and especially post-Timeskip that I would feel bad if I went through with the Lopunny gag.
-Usopp is going to catch one of the Pokemon you listed. He will also catch a ghost type Pokemon that I don't think anyone will see coming.
-If Smoker or Tashigi did catch a Wingull, it would definitely have Smoker's smoking habits.
