AO3 does have very nice functions nowadays for filtering out things you don't want, so it's not an insurmountable problem, just an annoying one that makes the browsing more difficult and so makes it more likely that I'll just hit my few most common relationship tags. But in the fandoms with adaptations (like Lord of the Rings) it must make things very confusing when you're looking for one version of the source material only. The Doctor Who issue seems to be with people not realizing those are meant to be two separate fandoms and therefore you should tag both only if it really is about both.

The Weeping Angels aren't a Classic Who villain, btw, Moffat invented them and Blink was their first appearance. :-)