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: Children Of Time
Complete Monster: Professor Moriarty and Colonel Moran, often referred to as such in-universe.
Family Unfriendly Aesop: Just about everything Beth does in the series is something that teens really shouldn't do, from tussles at school to tracking criminals down to their evil lair to... well...
Harsher in Hindsight: Given how much Foreshadowing there is throughout the entire series, this pops up with chilling frequency in the finale.
“Not if you do not wish to truly experience your role and sleep on the street...” Which Beth actually ends up doing while on the run with the Irregulars.
“I should have cuffed you to the railing back at Baker Street.” Holmes cuffs Beth to the cab door just half an hour later, which starts the ball rolling on a world of trouble between the two.
Not to mention the use of Vincent Starrett's poem as a Motif for the finale. You will never think of the words "always 1895" the same way again.
Robo Ship: While there's definitely Doctor/Rose here, the Doctor/TARDIS is also quite blatant.
The Woobie: The Doctor's woobie status is solidified very early on in the very first episode. Holmes undergoes serious woobiefication by the middle of the series, and Watson reaches that status in "Watson and Sparrow" (CoT's version of "Blink"). Sally becomes more of a woobie in her introductory episode. Then Beth re-enters the equation and probably ends up trumping them all until Holmes undergoes Cold-Blooded Torture. Even so, Beth remains the only one who actually dies.
Jerkass Woobie: Holmes in spades in "Dynamics of a Point", though it really starts in "Watson and Sparrow" and picks up traction in "Fractures".