Damn near everything about the Mask of Ice aka Pryce and the backstory about how he kidnapped children, forced them to wear masks at all time, and put them through Training from Hell in order to use them as tools in his plan to gain control over time.
The artist said that he was a fan of monster and horror movies, and that he wanted to incorporate as much of it as possible in the final battle of the RS arc; at certain parts, it shows.
The mere presentation of Archie and Maxies orb-inducedSanity Slippage and subsequent possession by Groudon and Kyogre is enough to scare you, with their looming shadows and deranged expressions, nevermind its full implicationsexacerbated by the fact that its never really made clear just how far gone they are until theyre already at the point of no return.
Especially supplemented by the horrified reactions of Tate and Lizas grandparents, the guardians of the blue and red orbs.
Maxie setting Norman's corpse on fire during the final battle of the RS, right for Ruby to see. Can you imagine how Ruby felt, having already seen his father die in his arms?
After forcing the Orbs out of Archie and Maxie in RS, Ruby and Sapphire wind up on Mirage Island, where Juan reveals that their efforts were only a temporary solution and that 21 days have passed in the outside world. Let that sink in for a moment: 21 days of Groudon and Kyogre fighting nonstop, droughts and floods all around the region and the Gym Leaders and Elite Four doing all they can to contain the damage. Twenty. One. Days.
Team Galactic is much more sinister than they are in the games due to the grunts being all Brainwashed and Crazy as part of a Hive Mind, and basically act exactly like how Cyrus wants to reshape all of humanity into: cold, emotionless, robot-like beings who only exist to perform their function.
The ending of the HG/SS arc. Giovanni is able to get his medicine and helps save the world... and then reveals that he was Evil All Along and leaves Silver behind to rebuild Team Rocket, giving Gold and Silver an offer to join him if they wish. It just goes to show that even if he's a Noble Demon who loves his son, he's still a megalomanic criminal and this may never change.
The ending of Black/White. Ghetsis gets off scot-free and Black is absorbed into the Light Stone.
By the time the B2W2 arc starts, which is set two years later, he's still in there. This means that Black's been a rock for far longer than Red, Green, Blue, Yellow, and Silver have.
Hell, Ghetsis in general. His Faux Affably Evil front from the games is taken to an even greater extent in the manga, and to see him act so polite and kindly while doing the most vile, sadistic things is just completely unsettling.
Unlike in the games, rather than just Opelucid, multiple cities are frozen with the Plasma Frigate's Kyurem Cannon, starting with the most populated one, Castelia City. And we actually get to see people frozen solid. As of current, Rood states about 70% of Unova is now frozen.
X/Y opens with the protagonists' hometown being destroyed.
Shauna having a Honedge forced into her hands while a Aegislash is looming behind her. Which means she's simultaneously being brainwashed and having her life force drained out of her.
She may have been really Essentia in disguise and wearing a helmet, but the sight of Y's head being crushed by Pinsir's claws is terrifying.
Judging by the pools of blood by their heads as well as everyone else's reactions, Lysandre and Malva were likely killed in the final battle.
The XY arc in general is one of the series's darker arcs, what with Team Flare attacking the kids nearly every chapter and how they have spies everywhere, leading the protagonists to realize that they have no one to trust except themselves. It's basically Paranoia Fuel: the Arc.
After all of the Jerkass things she pulled throughout the entire story arc believing she's The Chosen One, Zinnia gets her Laser-Guided Karma when Rayquaza shows its discontent and confirmation she isn't by stabbing her in the stomach with its tail. Then, when she still dares to convince it that she's The Chosen One, Rayquaza shoots her point blank with a Hyper Beam. Luckily, she survives to have her HeelFace Turn, but damn, that had to hurt.
Upon losing a battle, Guzma proceeds to scream at himself while smashing his head repeatedly to the ground, to the point his glasses break and the pieces end up in his profusely bleeding forehead. He then gently thanks his Pokemon for their hard work and assures them that they'll all do better next time.