Pokemon is a good example of something sweet and innocent on the outside that is appropriate for the whole family, but when you look deeper and speculate about certain things it can get pretty creepy.
I mean, Lavender Town. I really don't have to say any more than that, really. But when we look at Lavander Town, we have to ask why do we remember it so much?
The first time I reached Lavander Town (in FireRed when I was eleven), I was instantly struck by the music. I didn't come across the original Lavander Town music because I never owned that game (I was barely a year old when it came out, so I was a bit too young to have grown up with it back then), but in the remake I remember thinking that the theme was really sad compared to every other song I'd heard in the game thus far. The whole plot with Team Rocket actually killing Pokemon threw me off a bit too.
None of the towns before that were even remotely dark or creepy, and none of the towns past that were either. Lavender Town stood out to us because it was so much different from the rest of the game. Also they never really go into all of the details about the Rocket Invasion. You don't really get a motive besides "Evil Team Wants Power" and you never learn about what the town was like before the invasion. That's left to the fans to speculate on in their own time.
I think that's part of what makes things in the first Pokemon Game that came out nearly two decades ago still an interesting topic today. They don't go all out with the dark/scary stuff, but they put just enough in for it to stand out but also still be mysterious.
I think if the ratings for the games were higher, there's a chance they might overcompensate with the new limits and go crazy with having dark stuff. The manga was definitely a lot darker than the games, and it has zombie Pokemon, corpses being possessed and dissolved by acid and Pokemon getting cut in half! :P It might turn off some people, and it might also lessen the intrigue of having the creepy things hidden in the games, since they would become more commonplace and more mundane.
TL;DR: Pokemon is a series that is outwardly innocent, with a few darker elements mixed in that stand out because they are either rare or hidden. If the ratings increased, and the amount of dark stuff increased too, it might lessen its value.