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Well, the way I see it is that people will always want to see new Pokemon in the games. That's the lifeblood of the series. I think we're at the point where creating these games will become more sustainable as Gamefreak begins the process of translating all of the previous Pokemon to a format that's future proof in terms of 3D Models and Animations. Pokemon is a modular series in terms of how the games are coded. I would imagine, a lot of code is shared and just altered per Pokemon. So, including the Pokemon in future games isn't really an issue.

I get what you're saying about getting lost with all the Pokemon but I don't think Pokemon is a series where you have to remember all of the Pokemon. Just remember the ones you like. I know most of Gen 1-3 Pokemon by heart but starting with Gen 4 I only know a select few. But the ones that I keep in mind may not be the same ones that others do, and that's what makes Pokemon special I guess. The series is going through some growing pains right now but it'll eventually get things right...I hope.