This is an interesting thread. Lots of reminders of creative decisions I wasn't a fan of, but had mostly forgotten. With apologies for the repetition, here's some of mine:
The events of Before Dishonor were a kind of derailment for a lot of reasons. It ruined any potential T'Lana or Leybenzon had coming off of Q & A, and damaged Kadohata (who unfortunately would eventually be removed from the stories as well) and made it feel like the TNG books would continue to have a rotating cast of characters who weren't Picard, Crusher, Worf, or La Forge. Greater Than the Sum managed to get it back on track for me, thanks to Chen and Choudhury. Having Janeway get assimilated, become the Borg Queen and commit atrocities, and then die, in a TNG book, was borderline offensive (I say this as someone who thought Voyager was not a very good show and Janeway's character was hard to like; oddly I've become a fan of Kate Mulgrew). Worf was very ill-served in that story, acting like the dopey rage monster of early TNG, and not a former Federation ambassador.
The Andorian reproduction crisis always felt like it dragged on and on. It wasn't very clear to begin with what the problem actually was, and it just seemed to be there as a perpetual looming deadline, and seemed to be resolved again and again only to return again and again. The Shar character was almost exclusively about that issue, and it made me uninterested in him at times, despite the fact that I loved the Andorians and thought the culture developed in the novels was rich and interesting.
The early DS9 relaunch brought in some new characters who I came to like a lot: Vaughn, Tenmei, Taran'atar, and to an extent Shar, and brought in Ro, and had really strong returning characters from the show. After the schedule fell off and the time jump happened, the series was barely a shell of itself. Of the main relaunch crew, only Ro, Nog, and Bashir remained. Ro was unrecognizable as station CO. Kira and Dax out of the main action was a poor decision for a sense of continuity with the TV series, and with Sisko sidelined (UGH) and Vaughn and Taran'atar out of the picture, there wasn't much left to feel like it was DS9 (show or relaunch) anymore. And then the station itself was blown up. I think I stopped reading the novels almost entirely once Bashir was the character I was supposed to follow. He worked fine in an ensemble, but as the main character?
The first Voyager relaunch novels were bland and took almost all of my interest in following those characters away. I still remember the crying bunny rabbit counselor. Beyer's books changed that in many ways, but instead of adding new characters to fill in the holes, it became way too much about the old guard. The one major original character I can remember, Hugh Cambridge, was a tiresome character from the start, and his being involved with Seven of Nine was god awful.
I agree with whoever said above that New Frontier should probably have ended with Stone and Anvil. I mean, throwing in another war in the gap? A year after the Dominion War? I think I kind of Peter Davided myself out by that point.
Titan's biggest error was getting rid of Jaza.
The other original series were mostly good. Vanguard had a problem with having no likeable characters in it, but it was still intriguing.
I don't know if this qualifies as a creative decision or not, but leaving so much of it in the hands of white creators always bugged me. The human characters (especially lower decks) introduced were often a bunch of Smiths and Joneses and McGees with the occasional Chang or Patel tossed in for diversity. This never reflected what I expected a future Earth to be populated with, and with the freedom of casting that novels have, it felt weird that it was still so dominated by white Americans/Europeans, who are already a vast minority in the modern age amongst all of world's peoples. I know some, like KRAD and CLB, were much more cognizant of diversifying their casts, and I don't think anyone else was trying to be exclusive, but it was noticeable.
And again, Sisko, UGH. The tone-deafness about what it means to be a Black man in the real world compared to random fictional sci fi character seems so obvious to me.
Let me counter those negatives with some positives!
The Star Trek universe was expanded and felt much more like a real place. I felt this was like a continuation of the DS9 show (my favorite of the TV Treks to this day) and how it purposefully eschewed the idea of events happening in a vacuum. I remember how I used to keep track of cross-story references and even contradictions. I'm not quite so crazy as I was then, but I can still appreciate the effort put into it by the writers and editors. It was so wonderful.
Going back to diversity, I really did appreciate the amount that was there. More women, more non-whites, more aliens, and the beginnings of LGBTQ+ representation. All bright spots. Maybe not as thoroughly as I would have liked, but, still noticeable and I'm grateful. Titan's whole diverse crew (in almost every way) was just so beautiful.
So many of the stories were amazing. There were very few clunkers among the ones I read; most left me craving more. While Destiny was not my favorite story over all, the origin and resolution of the Borg altogether was brilliant (not to mention introducing Aventine and its crew).
Lots of great original characters. Vaughn, Taran'atar, Tenmei, Choudhury, Chen, the Gorkon crew, Ree, Vale, etc., were all characters I came to care about. Some of the characters most neglected in the live-action shows (e.g., Chakotay) or who were very minor (e.g., Gomez) got a chance to shine.
And KRAD joked above about creating the Federation government, but the idea that this thing we are supposed to be rooting for, our "home", being an afterthought on the shows, never felt right. It was almost as alien as the cultures we were being introduced to. So much has been said about how Star Trek saw a future where humanity overcame its differences, and yes, that feels pretty absurd a concept at times (and why I shudder at ever trying to explore the economics of such a world), but being able to see how such a vast magical society functions, was a treat. One of the things I appreciated about the perspective was that humans hadn't become inherently better; we had broadened our in-group, and so we still struggled with the same kinds of issues we have in real life.
(I still hope Bacco shows up as UFP president in Picard.)