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.
Arc Fatigue: The Zenith of Things Tournament (Z.O.T.T.) arc. Begun in Last Order Chapter 25. Ended in 110. So fatigued that it's broken up by various sub arcs, some of which experience fatigue themselves(the Vampire arc, where just about all of Earth's backstory is revealed). Bewildering once you realize that the Z.O.T.T. was only supposed to be a distraction for Alita's infiltration of Ketheres.
Even more bewildering, in universe the Z.O.T.T. took place over the time of a week. While in the original 9 volumes 16 years went by. This is actually Lampshaded in chapter 93.
Toji: It's only been two months since we fought on Leviathan 1... But it feels like it's been years, doesn't it?
Base Breaker: Last Order in all its size and glory. Some fans (while usually noting its shortcomings) see it as a welcome addition to the series which brings in new faces, deepens the World Building and is generally fun to read. Other feel that it's an empty action-stuffed drivel that throws all the depth of the original out the window in favor of boring Flash Backs, Infodumps, mindless Tournament Arcs, and Monsters Of The Week.
Most iterations of Desty Nova have been amoral at best and have performed inhumane experiments on humans all for the sake of research on Karma. The latest incarnation, Super Nova, powered by two Brain Chips, direct access to Melchizadek, and an afro in his introduction betrayed the main characters and the other two clones of himself to AgaMbadi, and proceeds to gleefully tell Alita how LADDER is going to send down an army after the Z.O.T.T. to wipe out The Scrapyard and capture all people on Tiphares for their brains, just before destroying Alita physically and mentally by telling her her brain was replaced with a chip and deconstructing her body, causing her remains to fall down a shaft all while maniacally laughing about it and celebrating over her despair and sadness, disturbing even his other clones. When he asks if the clones would like to work together with him and they politely decline, stating that their methods have grown too different, he uses his power to kill NovaPod and would have killed Nova X if he didn't unplug communication. All in his introduction. That, and he has yet to have been seen eating flan, Nova's usual dish of choice and what was a considerable quirk of his, showing just how different and evil he is from the regular Nova. While various Novas have been Faux Affably Evil or Affably Evil, Super Nova is just plain evil.
Col. Payne, who is only 'on screen' for about three seconds before getting killed; however he stays behind as Alita's nihilistic dark side.
We have Rakan, a merciless serial killer/rapist Space Karate master who's wanted throughout the solar system. His recent claim to monstrous fame was brutally raping and mutilating the bodies of Elf and Zwolf, who survived thanks to their backup brain chips. He seeks to do the same to his current opponent Zazie. To be fair, Rakan wasn't always like this. His story resembles that of Phineas Gage, a real-life miner who, after an explosion shot a tamping iron (rod) through his left frontal lobe, became a completely different person with no impulse control. Although the story of Gage is questionable in terms of its accuracy. The information we have suggests that, while there was a change in Gage's personality, it was not nearly as drastic as people used to believe. The only accounts of any emotional instability are exaggerated and only refer to the months directly after his accident, while everything else we know about his later life seems to suggest that his personality more or less recovered after a while, as is the case with many injuries of this kind.
Even though Rakan is given a sympathetic backstory, the way it's written, Kishiro seems be trying to get the audience to feel sorry more for Rakan's family than Rakan himself, leaving Rakan free to be as much of a creepy, deranged weirdo as before.
Last Order runs on Crazy Awesome. This is the series that had the most epic thumb war ever conceived, featured a fight against a giant robot with a Wave Motion Gun installed on a massive Gag Penis, and gave the most evil and monstrous incarnation of Desty Nova a massive afro. There is no shortage of times when the series just revels in its utter insanity.
Tiegel the slowest Motorball player ever, winning a race because all other runners are too damaged from fighting each other.
A special chapter in the original about how scrapyard Cyborgs are made, shows Ido making a super fast stomach for Alita, resulting in her having a bad time on the toilet and calling him a bastard afterwards.
Everything Figure Four does is either this or CMOA.
Alita learning that Shumira got together with an ugly, short, fat but loving man with whom she has nearly a dozen children ranging in appearance from their father to their mother. Her reaction is priceless.
Alita seeing the DNA organ and having a sudden urge to play it. Thankfully the others can stop her.
Sechs, Zekka and scribbling seems to be becoming a Running Gag, with their last fight where Sechs was scribbling on Zekka himself.
After finaly meeting again, Alita makes Sechs the first person she reveals to that her brain was replaced with a chip making her a perfect duplicate of the real Alita. However instead of talking about what that means about their respecitve existance, Alita starts to apologize for every insult she thought about Sechs, by listing them all infront of Sechs. Double funny since all the insults are incredible childish including:
Alita: :I never even said the worst one to your face, I guess I should have. You have the personality of an egg plant.
Every omake strips. Highlights include the secret of where the material for Alita's blades come from, Zekka trying to destroy the environment with silly acts of pollution like taking plastic instead of paper bags or the Jupiter version of the cartoon show based on Mbadi's heroic actions.
Epileptic Trees: In Volume 3, Sechs notice something is wrong in Jeru when Elf and Zwoelf's little toys start flying away. Afterwards Elf and Zwoelf are completely in Mbadi's control. Several volumes later we learn that Elf and Zwoelf's brainchips are not in their bodies but the little toys they carry on their shoulders.
Foe Yay: Ridiculously implied in the impromptu fight/thumb wrestling match where Zekka does some serious hardcore flirting with Sechs. But then, Zekka's such an epic-levelmartial artist that it's entirely possible he can tell Sechs is a Gender Bender, just from the way he moves.
Fridge Logic: Ido and Desty Nova are doctors that often deal with cyborg brains, but in Salem where they learned their skills, no one has a brain.
All There in the Manual: Ido learned those skills in the Scrapyard, and at first had a distaste for operating on cyborgs. Only after the events of "Sweet Night"(Gunnm vol. 7.5), a heart-breaking experience with a runaway clone, did he start treating cyborgs as people.
It's very like they learned their respective skills via simulations considering the technology they had access to. Also Salem regular receives large shipments of organs including brains from the Scrapyard. It's like those are also used for medical training.
On the other hand, Desty Nova learned how to rip people apart and re-assemble them as he desired in pretty much the manner you'd expect from a sociopathic genius who'd cut open his own skull on a whim and without anesthetic just to make a point.
One of the contestants in the latest Tournament Arcis a mindless monster that attacks using its giant phallus. Which fires energy beams. The explanation for this is that the machine was created by beings who saw humans in the simplest way, reducing us down to what they thought was the basic human traits (eat, kill, reproduce) so they designed the machine with a giant phallus, a giant mouth and omnicidal behavior.
Kaos's epic Ouroboros-fuelled tripout features some amazingly nauseating and squirm-inducing visuals. THE BRAINS THING.
Venusian bioengineering has led to more Body Horror than you could possibly imagine.
The Woobie: Ed, Alita's Motorball manager. Too bad he dies a few chapters later.
Lou Collins, in a big way.
Alita herself goes trough so many horrible experiences she sometimes begs whoever has her at his mercy to just let her die.
What Do You Mean, It's Not Political?: The original manga takes place on Earth, in the Scrapyard, where just surviving day-to-day is a struggle. Space is implied to be a place of infinite luxury built upon their unwilling sacrifices. Last Order kills that concept dead as the dodo - space is every bit as horrible, just ruled by intrigue and Real Politik instead of the constant bloody duels of the wasteland. Isn't that what a lot of immigrants experience when they travel from the Third to the First World?