MewtwosAdvocate
The Last Supram
To me, the creepiest, eviliest place in pokemon was Lavendar Town in the GB version. Scary. ****. They really brightened and watered it down in the remakes.
I do believe that the first 2 generations were more "darker" then the most recent ones. It was probably because of the entire Team Rocket storyline. Like many people mentioned earlier, they did stuff like chop tails off of Slowpoke and such.
The more recent generations weren't as enjoyable. Ever since they tried to "kid" up the games to make the Pokémon franchise more appealing to a younger age group the main storylines get to be boring. I think this is why many people like the older generations more story-wise.