These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
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 a money-obsessed Jerkass in the Pokémon games. But his method of introducing himself in Pokemon Diamond And Pearl Adventure is to order his agents to suicide bomb a crowded stadium. Of course, it fails, but 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. Two of his organization's top officers leave to find the previous leader—Charon tries to kill them. Which becomes even worse when you find out that said previous leader is being held captive in Charon's base. And as a capper, that previous leader, who goes on to rally the remaining agents against Charon, had previously tried to destroy the universe.
Most of the running gags with the big-reared Galactic Grunt. Lucario nonchalontly poking the guy with the spike on his paw has to be one of the funniest moments
Most of the back pages of the books have a random Pokémon pointing out you're reading the book the wrong way, and Hareta translating in the form of "[Pokemon] says you're reading in the wrong direction!". Volume 5's example? An insane Cyrus glaring and growling at you. "Cyrus says you're reading in the wrong direction!"
Volume 6 also has Hareta tell the reader that his dad is saying you're reading it wrong, and his dad's reaction is something along the lines of "Quiet son! You're going to ruin my surprise appearance!"
Mitsumi and Mars going gaga over Minun in Volume 7.
Hareta calling Fantina 'Grandma', to her annoyance.
Cynthia sitting on a Galactic Grunt while Fantina's laughing her ass off over it in Volume 8.
Mitsumi claiming to have gotten lost due to forgetting how the warp panels connect in the Galactic Hideout in one the later volumes. Pretty funny whether or not she's telling the truth, as no one seems to believe her.
Jun yelling at Palmer for trying to flirt with Mitsumi.
Her Eevee (which Cyrus had kidnapped to make her cooperate) jumping into her arms afterward just makes it even better in this troper's opinion.
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 Special (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.