My gripe with Cynthia is actually the opposite: the Champion has the most right to influence the story alongside the player since, by all rights, they're the strongest authority amongst trainers in the region, as can be seen with Alder and Steven in the Delta Episode being consulted for the conflicts.
With that in mind, my issue is that Cynthia was played like she was a big figure when she really doesn't DO anything. In order:
- Blue has the excuse of not being Champion for most of the game, so he doesn't have that responsibility.
- Lance is absent most of the game, and only helps in the Rocket Hideout. Then again, Team Rocket is kind of pathetic in this game.
- Steven doesn't do TOO much, but in Emerald he is present for Magma's attack on the Space Center, which, in retrospect, is the only high profile activity by the teams before awakening their titan
- Alder does outright try to battle N, and is simply defeated.
Cynthia, thinking about it, just kind of pops up in places where Galactic shows up and does nothing to stop them: Veilstone right after you save the bike owner; Sends you to Celestic town rather than making the delivery herself, and doesn't do much after finding there's a bomb threat; Rowan evidently doesn't contact her nor does she investigate the lakes after Galactic bombs one; and then there's the infamous moment in the Distortion World. Also, Team Galactic publicly has a giant building for themselves in Veilstone, and nothing is done about this. This wouldn't be so bad if Cynthia wasn't one of the very few Champions that was legitimately challenging to fight; I give the manga credit here, since they had Cynthia fight Cyrus and lose to his tactics.
I never really got "edgy" out of Cynthia. "Edgy" tends to be a character that defies rules, their way is best, pushes boundaries in universe and on a meta level. Cynthia seems at worst like an Aloof Dark Chick, and barely at that. But despite being the first case where the Champion seemed written as an involved figure, Steven was more involved (if just barely and with less focus), while Alder was where they finally understood to actually have the Champion do something if they said they'd do something.
I maintain Zinnia as a Mary Sue, whereas Cynthia is unhelpful or a case of informed ability (story wise) until the actual Champion Battle.
Also, while I don't condone the idea of them becoming even more OP, Primal forms would be a possible way to mitigate the issue of the Creation mons' overpowered Pokedex abilites. Groudon and Kyogre were powerful, but their particularly ridiculous power levels originated from some supernatural energy that turned them Primal, which Rayquaza broke them from as a Mega. It'd mitigate the "Arceus is THE God" theory, since instead of creating the Universe from scratch, it would mean he and/or the Creation Trios merely harness/shaped an energy that was already there.