in volume 12 Ainz says all the time that he dreams about a nation in which all races can live alongside each other and is portraied as someone who doesn't randomly kill anyone without a good reason (so basically he won't needlessly kill the innocent), but then he proceeds to kill half a nation for no apparent reason except maybe information gain and making them immediately surrender to his rule? Although there would've been plenty other ways of achieving that??

to the point of actually writing 1-2 volumes mostly about him,

Arche dying after being saved by Ainz,

Neia who was basically the only topic the whole 12th volume was about being pretty much sentenced to death at the end and probably gonna die in the next volume

Evileye being foreshadowed of being killed off pointlessly some time in the future

and many more less relevant characters like Neia's father, Stronoff, etc.

of Neia dying a friggin pointless dead too, just because Ainz is too friggin dense to realize how much she admires him

The lizards are just mention in a single scene cameo and that is after 2 volumes from their introduction, I felt these characters should be at least have some more focus if the author spent time to flesh out their stories for one volume.

He still has emotions which I would think is suppressed because it was after all written there, then later he gets embarrassed and angry from riding a giant hamster. Further in Volume 7 he is enraged by some adventurers he lured, which he explains that his emotion is actually just cutoff after a certain threshold, meaning if he gets too emotional he loses the emotion which is retarded.

Don’t even try to explain the significance of him keeping that small town alive aside from the potion productions.

The closest analogy would be a story about ants like a "A Bug's Life". There are interesting powerful ants, there are boring insignificant ants. We learn much about the ants' daily lives, societal interactions, power struggles, dreams/hopes/frustrations. Then one day, a big clueless bumbling elephant comes along and accidentally stomps on the ants without realizing it. No, not like Saitama from OPM where he contributes meaningfully to characters' lives. Just stomping on them.
Rinse and repeat for 13 volumes.

- MC is quite useless. A former salaryman who becomes ridiculously OP, but is still incompetent and foolish even at 13 volumes. Zero character growth, he continues to be plagued by insecurities and is mentally weak. Very similar to Mushoku Tensei, although he isn't that much of a complete loser.
The concept of an OP main character isn't bad if it's done well (One Punch Man). But again, we've moved past the era of loser MCs.
The joke of plot armor and bumbling strokes of genius is so repetitive that you're already expecting it.

- Author tried to add a darker side to MC where because he is an undead, his emotions get suppressed due to a buff/debuff and somehow becomes a psychopath. It was very poorly written since there was no proper transition (a lot of commenters have indirectly mentioned). At the beginning he's mowing down villains and being a good samaritan. Suddenly he becomes a retarded psychopath like Trump with nuclear launch codes.
Loss of emotional highs/lows does not EQUAL psychopath. That's a poor understanding of human psychology. Psychopaths are defined by complete lack of empathy. The fact that a debuff comes on whenever he experiences highs/lows means he can feel. Even if he was a loner in his past life, it doesn't automatically mean he should act out on a power fantasy. There's just no justification provided on how and why he becomes a psychopath, and at the same time still act like an awkward bumbling fool in his interactions with other people.

- MC has a team of amazing talent under him, but cannot seek their help to perpetuate the myth of his invincibility. Very inconsistent with the fact that none of his subordinates cares since their loyalty is programmed in. This all comes down to weird Jap culture of "face saving" even if everything goes to shit. Very weak concept to sustain the whole novel.

- Author decided to really embellish side characters (mostly ordinary residents of New World), devoting multiple MULTIPLE chapters to create their backstories, way more than ALL of the primary characters. I get that author wants to establish different POV for readers, to empathize with side characters and realize how a lot of them end up as pawns in larger schemes (inadvertent or not).
Here's the writing problem. When you devote an INSANE amount of content to obvious side characters that don't advance any plot before killing them off, then it's not Game of Thrones, it's just a stupid WASTE OF THE READERS' TIME. It's a confusion of who the main actors in a story really are. And worst of all, most of them are killed off because MC is just a bumbling fool, which just leaves a bad taste.