Negi got a bit burned due to his wife giving birth, he couldn't handle an upcoming children with projects like some mangaka could (best recent example being Witch Watch), combined with having a retard for an editor (now his best strength for his shitty Ranger Reject manga), so the ending got rushed to all hell, it really reads like he took 3-4 arcs & mashed them together to make the final arc. Other than that, the biggest issue is how the end reverses the development of most of the cast so it feels like nothing in the story really mattered, the end plays out as if the author wrote it before the manga & then just paste it at the end without taking into account how the story actually developed.
Waifu-fagging
This is something I'm also guilty of (Nino my beloved) tho I only say this as someone who only saw the 1st season when it was airing, before being spoiled on the series before S2, but people disliked the girl that won. Yotsuba (we'll call her 4) won, but the other sisters 1, 2, & 4 had more screen-time & development by then, meaning that the already extremely rushed feeling 2nd half of the series (which was S2, movie was finale) are now ruined. 80% of the manga could be considered spent doing nothing, the "development" was fucking flashbacks all the time.
Also, 4 is as pity-victory as it gets, she has the least interactions with the MC. She got forced into relevancy last minute (could've been worse, like a D.Gray-man situation).
Turns out, the reason was Negi himself was waifu-fagging, except he was doing it IRL cause Yotsuba was based of his own wife. Also, this shit got leaked by the editor 6 months ago, but most didn't believe it then or huffed copium. This means that the ending was decided at the beginning. Negi created the story around the ending, not the kind of work that writes until the end to come up with an ending. Issue is, Negi was so obsessed with making it a mystery that he pretty much had to leave things regarding how the MC felt as ambiguous as possible. The proof of that is how it ended. The mystery gets solved & 2 chapters later the manga ends, ending with a half-hearted reassurance that yes, he knew the girls.
To make it even worse, he nearly got death threats for the ending. Nips on 5chan were shitting on Negi & 4, the Sakura Ayane shitpost (I'm not explaining this, it's too retarded to explain) originated from there. Negative Japanese Amazon reviews were posted on /a/ to show how bad the writing was for the characters, Negi's handling of the mystery of the bride, & portrayal of Futarou's feelings. In fact, Aka Akasaka admitted to not liking the ending either in an interview in a magazine prior to the release of Kaguya-sama S2, apparently he could tell Yotsuba was gonna win the second he saw her in the manga.
Incendiary Actions
Before going into this, I'd like to clarify that Negi isn't some pretentious, pseudo-intellectual, lolcow mangaka like Aka Akasaka (Kaguya-sama, Oshi no Ko), Makoto Yukimura (Vinland Saga). He's not a scorned mangaka like Shuwata Ramunewura (Gal ☆ Cleaning!). He's not a troll mangaka like Akira Hiramoto (Prison School, & literally every other work of his)... He's just a guy who tried to "deconstruct" to the point of disliking his own work & simped for his wife a lot.
Now to those incendiary actions, one of those was the thank you note, mainly the lack of it. Negi didn't even write a note at the end of the last volume to thank the readers for support, something which is customary among mangaka, even doujins artists do that.
Another one was that he didn't publicly acknowledge the ending of his manga, to make it worse, no one from Kodansha publicly acknowledged the ending of his manga either. He also forgot to make art for Quints' brirthday & had to shit out some scribbles at the last second.
He also admitted drawing headphones for Miku was annoying, which Miku fans didn't like. She was also expected to win due to first girl rule, but the deconstruction killed that notion.