All of those things should have already been explained in the story. If there's something different about your characters, it should be mentioned in the narration somehow. Since you didn't mention anything about Chaos being different from normal human beings in the story, the readers assume that she is normal and ask questions. Just like with her having weaker Pokemon. Mention that in any way in the story. Even just have her say "Oh darn, I don't have my best Pokemon with me."
When your readers start your fic, they go in expecting it to have some basis on the world (or "canon") that they already know. If you want to change some things from how they are in canon, that's okay, but you really need to explain it. Like with Oak being one of the strongest trainers. Canon says that Oak doesn't battle anymore. He's more focused on his studies. Changing him in your story from what the reader knows requires explanation. Why would Oak pick up battling again? Why are Magma and Aqua operating under Rocket when canon says that Magma and Aqua are their own teams?
While it's nice to know that some questions have answers, it's better to already have had this explained in the story.