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 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.
Complete Monster: 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.
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.
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 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.
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?
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.