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Pokemon sales have largely stabilized at about 16 million for the first games in the generation since gen 3.
This suggests that there's some kind of market stability, where for every person that checks out, roughly one new person checks in.
Broadly speaking, people who buy pokemon can be broken up into three groups: children and the parents that buy their games, people that like video games and play Pokemon because they're good games but aren't super invested in the series itself, and more hardcore fans that are really into the franchise. Historically speaking, it seems likely that for every kid that checked out, a new one checked in, and the same for their parents, "softcore" fans, and "hardcore" fans. Taking each group into account:
>1. Parents and children don't really give a damn about controversies like this, and the few that do probably won't have a big impact on sales.
>2. Softcore fans may either care about quality or just buy a big brand, so some will likely be turned off at a higher rate than normal.
>3. The hardcore fans are clearly split on these games, and the controversy probably affects them the most.
Basically, Pokemon has had similar leave/introduction rates because its worst controversies before this have largely been centered on new pokemon looking bad, which was wholly subjective anyway, and if it caused one person to stop buying the games another could easily fill their shoes. This is different, and it seems like a lot more people aren't going to buy the games, meaning that it will be harder to fill their shoes in turn. Both softcore and hardcore fans will have a notably larger chunk of people check out this time, but that's not enough to cause massive damage to sales, just notable, since kids and their parents are basically unaffected by this. They also cost a bit more, which even for a franchise like Pokemon will hurt sales to some degree.
TLDR they'll probably sell less than normal