There's also a huge inconsistency between the book and movie's ending, where in the book the Ex Machina fight the Flugel to the bitter end until most of both races are dead and they slay Artosh offscreen. The author doesn't think this is an issue but in a story as fast as NGNL any pacing interruption matters a lot, I think, and that arc is still ongoing too so if they were to try and fix the inconsistency they wouldn't know how.
Then there's the scrappy Emir Eins who is not only worst girl but she talks like an Ex Machina but unlike Shuvi she doesn't do it sparingly, which is fine in a book where you can skip the "[Initiating dialogue mode], [making inquiry], regarding recent events, that is, [unnecessary explanation], if Sora[non immanity human] and Shiro[..." but to have it spoken in an anime would make the staff and audience hate every second of screentime, which she has a lot of because the author clearly thinks she's best girl. The VA would hate herself too.
And of course there's the content. Art is art, but even ignoring the difficulties in publishing there were times I thought brought down the vibe; not a content example but the siblings being kind of assholes to their friends who throw them a birthday party just felt off, like reading a fanfiction.
And in that vein Sora acts like he wants to have sex in the first season and moments like when he makes Steph love him are great, but especially after Emir Eins shows up and endlessly demands to have sex with him he's always acting like your usual boring male protagonist going "whu-whu-WHU-WHUUUU-WHUAAAAAAAAT?!?!" and the author has an ongoing arc for Sora he keeps suggesting but he drags it out forever and it continues after it should have been resolved. Basically he thinks he tricked Shiro into dropping out of life with him so he doesn't believe anyone could actually like him.
But maybe the main thing is the story starts out with the darkness of society, something hard to express which the author manages by just showing you the siblings and saying, "you get it, right?" and they're sent to another world in an adventure with incredible momentum, but over the years the books have been ongoing the author loses that important sense the world has as well as the momentum and never touches on the same themes, despite the new world being darker than the one they came from. There's something about old racial hatred from a world war that people can just accept, like violence is strangely clean, but the purple haired little girl from the movie who's dad dies ends up getting kidnapped and enslaved by elves and she and her descendants are raped for thousands of years but after everything Sora/Shiro has been through and stand for are they just gonna play a chess game against an elf and move on? Jibril did nothing wrong.
Also Holou being introduced as the third member of Blank with actually great chemistry and immediately banished to the shadow realm in favor of Emir Eins is a huge disappointment.