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.
Angst? What Angst?: Train in the later half of the manga. He gets shot by a bullet that is known to transform people into monsters, yet just shrugs it off (despite everyone else including the Big Bad panicking). When he turns into a kid, his first thoughts are that it'll make meals and bus tickets cheaper. When asked if he's concerned that Creed is trying to bring about the End of the World as We Know It, he answers no, and that he's mainly concerned with what's for lunch.
Complete Monster: The unnameddoctor, a sadisticmad scientist with a penchant for human testing, conducts a number of awful experiments over the course of the series, transforming a man into a werewolf, brainwashing captured bounty hunters into fighting their friends, and trapping Train in a illusory world where the very people he cares about most are trying to kill him. Fascinated by ten-year old Eve's power to shapeshift, The Doctor kidnaps her towards the end of the series, planning to vivisect her in order to discover how her abilities work. Loyal only to himself and driven by his need to know, The Doctor outshines even Creed Diskenth when it comes to villainy.
Compressed Adaptation: The anime, which removes whole arcs, completely rearranges the whole start of the series, and cuts a lot of character development for everyone but Train and Eve, or distilled in a very awkward way. Which is strange considering that the anime is also an example of Adaptation Expansion.
Tendencies? The man has exactly zero qualms about killing you if you "stand between me and Train." Given his obvious propensity for seeing things obsessively... does anyone here have a mathematical formula for how long it would take for Creed to end up killing the entire world's population out of jealousy?
His lack of eyebrows cannot be excused.
Some Apostles naturally get this treatment. Shiki's nearly morally bankrupt, but s/he's beautiful. Charden has done terrible things on a vengeful crusade, but he's such a gentleman. Kyoko's an obsessive, psychotic pyromaniac, but she's so funny and adorable. Echidna's a conniving bitch, but she's sexy. Durham's a Trigger Happy psycho, but he's so cool. Leon's a budding psychopath himself, but he's such a cute little kid. And the Doctor...wait, even fans know there are no excuses for that asshole.
Also Shaolee, who spends his time deceiving people, is actually one of the cruelest Numbers and is quite creepy when you think about it, but looks just so pretty.
Evil Is Sexy: Echidna, although she oddly never makes use of it. Kyoko too to a lesser extent. As for male villains, Creed, Shiki, Charden, and even the Doctor are very attractive.
All of the Yaoi Fangirls want to see Creed and Train together. (Well except for the small amount that go for Sven/Train.)
While Train/Kyoko has it's own following, Charden/Kyoko seems to be even more vocal.
Fashion-Victim Villain: Nice jumpsuit, Creed. Did it come with the open chest, or did you cut it out yourself?
Foe Yay / Ho Yay - The romantic / sexual tension between Creed and Train. Though it's rather one-sided, as Train clearly has zero intention of returning Creed's affections. In fact, he doesn't even seem be aware of them, which isvery impressive.
It Was His Sled: If you start the series through the anime, what happens to Saya should be obvious due to the huge amount of foreshadowing in the opening and ending.
Creed murders Saya simply for the humanizing influence she has on Train. And after suffering a nasty injury that might have made people sympathize with him, he then tries to turn Sven into a mindless monster.
When facing down Sven, Torneo is all ready to use a nanotech drug on Eve to force her to become a mindless killing machine. Train shoots it out of his hand to stop him.
All of the Doctor's experiments put him far over the line.