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In the post game of several games, there are trainers that are stronger than the champ, as well as wild Pokemon that are just as strong or a little weaker than the champ. Is this just GF logic, because it seems to me that the Champion and their Pokemon should actually be the strongest Pokemon and trainer in a region. So is there an explanation for this, like: Those trainers choose not to compete against the E4, or are quiet/timid, or is this just Game Freak Logic pulling another one.

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Game Freak Logic.
You seem to have answered your own question.
Sorry, I'll hide it, if you want me to HT.
Nobody really knows for sure except Game Freak themselves, but I think it's because they wanted to make an iconic final boss character. Why would a generic [insert common trainer class] be the final boss of a game?
Was this downvoted for being answered in the description like HT said? If not, please tell me why so I can fix it.

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It’s Game Freak logic.

But, logically, it’s for the levels to be scaled to yours. Would we want a champion with level 80 Pokémon if we had levels in their 50s? Of course not. Would we want weak trainers during the post game that we can easily run right over? Nope. Game Freak doesn’t strive to be the most logical game, it wants entertaining games that it can sell. Would the TV show be fun if Ash lost every battle because of his weak Pokémon? No. Would it be more fun if he won some? Yes.

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I would like to disagree with the last part of your answer. Ash should lose due to his bad pokemon, train and grind like real people, and throw pikachu out of the building for a better mon like a legendary or a starter. Him endlessly training and grinding would be more relatable , and be a better story arc. Although it might be a bit cliche. And it might be less attractive to kids of young age. Still...... it would be more entertaining this way.
“And it might be less attractive to kids of young age” the anime is pretty clearly aimed towards younger children in my opinion. I don’t think children would like to sit through Ash training when there could be an exciting battle. Excitement sells better.

My point is, it wouldn’t be exciting if there was tons of logic. Games that aren’t as exciting don’t sell as well, and of course Pokémon wants their games to sell well.
Thanks Primal!