Compared to other continuities a few characters are this. Candice stands out, being The Ojou and much more stoic than her other counterparts (which are typically Genki Girls).
Cyrus is also a lot more expressive and zealous in this incarnation, even though he still claims to disregard human emotions.
Badass Decay: Regigigas. After the huge buildup it gets, it fades to be really about as powerful as anything else Hareta has, and no one has any reaction to him having a legendary ancient guardian. The bit about it being as strong as Hareta's other Pokémon may be justified by the fact that its Slow Start ability gets mentioned several times, which does bring down its battle potential in-game quite a bit. Hardly anyone commenting on it being Legendary after its initial appearance, on the other hand...
Complete Monster: Charon was always a money-obsessedJerk Ass in the Pokémon games, but here his method of introducing himself is to order his agents to suicide bomb a crowded stadium, the explosion potentially destroying the whole town were it to spread. While this fails, his intent is clear. He holds no regard for the lives of others and plans to control the world with money made from selling legendary Pokémon, as well as to extort more money from the masses by threatening them with the power of Giratina. He also does nasty experiments on Pokémon that shuts off their very hearts and essentially turn them into living weapons, Koya's Growlithe being among his victims, and we see him use a bunch of Skuntank under Mind Control as explosive weapons against the opposing trainers. Charon doesn't even treat his colleagues within Team Galactic well, as he captures the organization's previous leader, Cyrus, and tries to kill two of his top officers when they leave to find him. Cyrus goes on to rally the remaining agents against Charon, despite he himself previously trying to destroy the universe. Thinking only of himself the whole way through, Charon ends the series the sole character to reject The Power of Friendship as a concept and thus ends up thoroughly irredeemable.
Her Eevee (which Cyrus had kidnapped to make her cooperate) jumping into her arms afterward.
Cyrus telling Mitsumi that the final battle is only for Team Galactic, which she's no longer a part of. Effectively freeing her from her bonds to them. Although she had already been trying to do so, that he finally realized it and, after all those years, did what was truly right, makes it doubly powerful.
The final battle with everyone fighting together. Cyrus's smile alone makes it. Compare his relaxed expression there to his incredibly creepy genuine smile in volume 2.
Ensemble Darkhorse: In a franchise where the only manga most people know is Pokémon Adventures (with the occasional anime adapted one), this series stands out due to its notability and access. Just look at the size of this page. Part of this is that this series actually got released in America in recent times when manga is more popular, so people actually now knew it even existed.
Evil Is Sexy: Everyone in Team Galactic except Charon is incredibly hot. Even B-2 if you ignore his most prominent feature.
Foe Yay: Cyrus's interactions with both Hareta and Mitsumi are made of this. Then there's Jupiter's interactions with Mitsumi. To a lesser extent, there's also that chapter with Koya and Mars...
It Was His Sled: That Mitsumi is a former Galactic member. The covers even spoil it.
Les Yay: Cynthia's obsession with fighting Mitsumi.
Charon accomplishes this before he even shows up, what with the would-be suicide bombers ready to take out a crowded stadium basically because he told them to, and the explosion could potentially wipe out the entire town were it to spread.
If that didn't cement him as an unforgivable scumbag, then his experiments on Pokémon to turn them into living weapons, including making a bunch of Skuntank suicide bomb themselves to attack the opposing trainers and trying to have Koya's own Growlithe (under Mind Control) kill Koya, definitely seals the deal. And on top of that, he's also responsible for the out-of-control Onix from the first chapter and giving Cyrus the idea for one of his biggest Kick the Dog moments.
As always, Cyrus' plan to, with godly powers over time, obliterate the universe and kill everyone and everything in it before remaking it all. Unlike Charon, he actually manages to come back around from this, though.