These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Author's Saving Throw: The New Adventures offered two different explanations of the Sixth Doctor's perfunctorydeath and regeneration. The first was convoluted and wangstynote In short, that the Seventh Doctor, "waiting" in the Sixth's mind, allowed the Rani to attack the TARDIS and bring on the regeneration 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.
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.
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, 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.
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 childrens' 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.