So, what have you noticed that's wrong about Pokémon in general? Doesn't have to be from a specific game, but what have you noticed that ruins Pokémon's reputation for being reasonably innocent and meant for little children?
I'll start.

Why IS the reception lady watching you while you change clothes for contests/Pokéathlons anyways?

Oh, and let's not forget the old men asking little girls for their phone numbers in HG/SS.
"Let's be friends!"
Yeah, right.

And also, when you get an Egg at the daycare, the old guy says...
"We were watching over your Pokémon, and goodness, were we surprised! Your Pokémon was holding an egg! We don't know how it got there but you want it, don't you?"
Note the bold text.
....Sure, you don't.

Metapod being shaped like a penis.

You forgot Kakuna. And Barboach.

Oh! Yeah! Speaking of Barboaches, there's these two guys in Sootopolis in R/S/E who want to see big Barboaches and Shroomishes.

Well, uh...that's nice.
(Thanks to the Cave of Dragonflies for pointing this out)

When you encounter your rival in Lavender Town he asks whether or not you know what it's like to have one of your Pokémon die. At this point in the game, he no longer has his Raticate that he used in previous battles.Your rival battle before this took place aboard the S.S. Anne. Your rival's Raticate sustained serious injuries from the battle...but, because crowding and confusion on the luxury liner, he was unable to make it to a Pokémon Center in time and the Raticate passed away. The real reason your rival is in Lavender Town to begin with is to lay his deceased friend to rest.Despite all of this, your rival never outwardly tells you that you're responsible for the death of his Pokémon. He hides his grief and instead channels that energy into the motivation he needed to continue his quest to become Indigo League Champion.

The death of his Raticate effectively destroys your rival's impish, childhood innocence. Although he tells himself that he doesn't hold you responsible, he subconsciously holds a great deal of resentment towards you which further fuels his ambitions.Tearfully swearing upon his Raticate's grave to not fail in what he set out to do, he trains hard in hopes of becoming better than you...defeating you...and to eventually make it to the Pokémon League. Mere moments after he became Indigo League champion, he was defeated...by you. Although he fulfilled his promise to his fallen Pokémon, it was only for a painfully brief instant.In the end, your rival is scolded by his grandfather while you receive the professor's praise.

During the course of the game, you steal your rival's innocence, crush his dreams, and ultimately snatch away the love of his own grandfather. Oh, and by the way, your rival doesn't have any parents. He's an orphan.

i love how you can go into random peole's houses and they don't rwally mind

To Kyta: Hmmm. Dramatic.

To Katra!: Yeah, that's hilarious. In real life, people call the cops on you.

In SS, in the Poison Gym in Johto, there's a dude dressed as the Gym leader(who's a girl) and he says something along the lines of "What? There's nothing wrong with a boy dressing as a girl!"

wat

wat

Nope, nothing wrong at all. </sarcasm>