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Not to intentionally regurgitate a Sinnoh fan’s opinion, but from what I’ve seen, Cynthia seems to be the most popular non-playable trainer in the franchise. Even her theme and its variations have a moxie of their own. Game Freak tried to home-brew Leon’s popularity and infamy before Sword & Shield came out, but he comes nowhere near the levels of adoration Cynthia experiences, because players claim Leon’s hype felt “artificial”, as opposed to Cynthia’s.
So, with that said, why has Game Freak been shy about showing Cynthia since the skip to 3D? Sure, she got a cameo in Gen 7, but it felt incredibly minor compared to her presence in Gen 5.