- Author's Saving Throw: The New Adventures offered two different explanations of the Sixth Doctor's perfunctory death and regeneration. The first was convoluted and wangstynote and firmly squished by the second, which dismissed it as an impossible story the Seventh Doctor had subconsciously persuaded himself of because he, The Chessmaster, couldn't face having died in such a pointless and random way.
- Dork Age: The second half of the series, when everything got so much Darker and Edgier it was difficult to recognize it as Doctor Who; Ace was converted into a '90s Anti-Hero, the Doctor was increasingly flipping between being a Demoted to Extra Pinball Protagonist or a batshit insane Machiavellian Knight Templar it was difficult to root for, and many of the best writers of the Frocks crowd, like Paul Cornell or Gareth Roberts, had stopped writing books for the line. TV companions from earlier eras like Liz Shaw and Dodo were getting Stuffed in the Fridge in Narmfully mean-spirited ways while others were getting Revisioned as child rape survivors or catching space-STDs, and production problems led to So Vile a Sin, the book that killed off Roz, coming out after the books in which she was dead.
- Ensemble Darkhorse: Benny. In spades. A companion for roughly two-thirds of the novels, she would later be the focus of more novels once Virgin lost the Doctor Who rights, then of a Big Finish audio-drama series. Most recently, she met the Twelfth Doctor in the 2015 novel Big Bang Generation (her inclusion was a last-minute substitute for another Adventurer Archaeologist, River Song, when Gary Russell couldn't use that character because it would have contradicted that year's Christmas Episode).
- Growing the Beard: Opinions vary, naturally, but typically around the time of Benny's introduction and/or Ace's sojourn away from the TARDIS is when the quality started to level out somewhat.
- Harsher in Hindsight: In Happy Endings, written in 1996 but set in April 2010, the aging Brigadier Lethbridge-Stewart is dying of cancer and hoping to keep living for another year. Fortunately, in the course of the story, the Brig is rejuvenated and does not die. Sadly, in Real Life, the Brigadier's actor Nicholas Courtney died in February 2011 after a long battle with cancer.
- Hilarious in Hindsight:
- Human Nature features a cameo by Steven Moffat as the school bursar.
- The novel has one of the Aubertides tell Bernice he is the 10th Doctor, but she realises he isn't the Doctor as he eats meat. Later the 10th Doctor would be in the TV version of Human Nature, by which time the Doctor was no longer a vegetarian.
- The mention of "Councillor Ph'Roch" in First Frontier would just have been a throwaway pun at the time. But since the publication of Monstrous Regiment, it's got an additional aspect — Ph'Roch is yet another military officer with an item of clothing named after him.
- Internet Backdraft: The Looms. Oh Lord, the Looms. Cat's Cradle: Time's Crucible established that the Gallifreyans had been made sterile, and now used the Looms to create new Gallifreyans by combining their biodata. This did not go down well with a good chunk of fandom. They only showed up in a few books - Time's Crucible, Human Nature, and Lungbarrow - but the reaction... Gallifreyan reproduction is Serious Business.
- The New Adventures were never strangers to fan controversy and arguments; they introduced new and more 'adult' elements to the series, made the Doctor even darker and more of an Anti-Hero than he had been previously, adopted new spins and perspectives on the mythos and presented new ways of telling Doctor Who stories, many of which didn't sit well with the fan base at the time and caused a lot of online arguments. Unlike the Looms however, which still can cause punching fights to this day, with many of these other controversies it's often hard to see what all the fuss was about when looking back, as many of these elements have either been successfully incorporated into the mythos of the show as a whole and no one questions them (in the case of the ones that worked), they've just been gradually forgotten and ignored (in the case of the ones that didn't) or they just look a bit dated and silly to contemporary readers.
- Rescued from the Scrappy Heap: No Future, the novel that served as the series' 30th anniversary special, brought back a villain and an alien race that were regarded by the fandom as ludicrous jokes, teamed them up, and showed how dangerous they could be in the right hands.
- Ron the Death Eater: Does this to the Sixth Doctor.
- Tear Jerker: The denouement of Love and War. Watching the relationship between Ace and the Doctor disintegrate is brutal.
- What Do You Mean, It's Not for Kids?: Many bookshops shelved the first few novels with the Doctor Who Novelisations in the children's section, until Virgin pointed out that the way the novels were developing meant that it wasn't a good idea. Reported to have been consciously averted by Russell T Davies when the BBC wanted to reissue Damaged Goods to take advantage of his fame as the Show Runner of the revived series - he flatly told them that he didn't want child fans of the TV show reading it.
- Woobie, Destroyer of Worlds: The Monk. In No Future, just not so successfully at actually accomplishing this.
YMMV / Doctor Who New Adventures
WARNING! THERE MAY BE UNMARKED SPOILERS!