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.
YMMV: Virgin New Adventures
Author's Saving Throw: The New Adventures offered two different explanations of the Sixth Doctor's perfunctorydeath and regeneration. The first was convoluted and wangsty 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.
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.
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.
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.
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.