PokéBase - Pokémon Q&A
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Team Rocket doesn't appear in every game because the anime isn't canon to the games. If you've ever watched the anime, you'll notice that it's a lot different from the games. It doesn't follow the same battle rules, Ash doesn't follow the same order of where he goes as a trainer in the games would, there are some places that exist in the anime only, etc.
TL;DR: The anime isn't canon to the games.

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This is because the games have different stories and wouldn't fit Team Rocket's motives. In the games Team Rocket wants to take over Kanto whereas other generations (regions) have stories with evil team that want to do things like flood the region, liberate all Pokemon etc. which aren't things Team Rocket would necessarily be interested in. Comparing this to the anime the main Team Rocket members we see in each region (Jessie, James & Meowth) have the main goal of stealing Pikachu to give to Giovanni which isn't a story element we see in any of the Pokemon games except for Pokemon Yellow version which was based on the anime. (So at least there was that.) It's also probable Team Rocket won't show up in the anime after Ash's story finishes since it's his Pikachu they're trying to steal with the only exception I can think of being a flashback of some sort to a previous region.

Hope I helped :)

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Because the anime is illogical and doesn't follow the games.
As Hellfire Taco said, the anime and the games has a lot of difference. In the anime, level and base stats aren't existed. In the anime, Cilan can keep the sun in his bag (he can keep lot of table , spoon, frying pan and many other things for cooking) . In the anime, Pikachu can learn Volt Tackle for saving May' s egg, Aerial Ace can be missed and the anime has a lot of errors.
Team Rocket is always in the anime because the anime creator keeps Team Rocket for joke, gag. Such as, they thought Nebby is the pre evolved form of Koffing. They doesn't appear in every games because each generation has at least 1 exclusive new evil team (Gen 2 didn't include any new team). Btw, you can find every evil team in USUM. Gamefreak doesn't want to keep 2 evil team in a game (without USUM)
because the anime and the games isn't same

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In the Pokemon games, you can also keep 99 iron balls in your bag.