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It felt like the popularity was the biggest in 1st generation and it was recovered in 6th generation with Twitch Plays Pokemon, GO and Pokemon XY. The worst time for this franchise was between RS and DP. Kids grew up and some charm was lost - a pretty natural thing. And RS, despite what Hoenn lovers may say, didn't help (due to missing features and lost connectivity). After RS, there was a really long waiting period until DP came and gave the opportunity to trade globally.
Nowadays, Pokemon is in a good spot. Hype spreads extremely fast on the Internet. Fanbase just needs some content from time to time. I would love to see some spin-offs but they are known to not sell as well.