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I understand that everyone just wants to be able to have their favorite Pokemon which is an argument for the national dex, but if you really like Pokemon, you should be able to find plenty of likeable options in each dex. If you can't find a workable selection of Pokemon out of 400, I find it hard to imagine you're an actual Pokemon fan. You can only use 6 Pokemon in your party at once. You can only actually fight with 1 Pokemon at a time, or 2 in doubles. It's just putting so much effort into bringing so many Pokemon when the reality is that a large chunk of them will go unused by a large percentage of players. Also adding 1000 Pokemon just so people can have the ONE Pokemon they like, it's surreal expectations, really. Even more so if you start to think what happens when they have like 2000+ Pokemon.
It's better for them to get people on this new direction sooner than later. Are national dexers still going to sit and say each game is trash because not all 5000+ Pokemon are not in it down the road? Also look at Digimon. Digimon has over 1000 Digimon, and in games they do not have all 1000 Digimon. Cyber Sleuth only has 240 Digimon and it's considered a great Digimon game. Nobody even had expectations for all Digimon to be in even though Digimon have the same likeable factor and appeal as Pokemon do. If you gotta hinge your entire enjoyment on if a certain Pokemon is in it or not, I feel like you are playing the game with a barely visible thread of interest, because each individual Pokemon plays such an insignificant role in the game that you could choose to play the whole game without ever even using them.