The premise of Doctor Who is gloriously limitless in its imagination, letting us immerse ourselves in unadulterated escapism (depending on the BBC budget of course). As the Eleventh Doctor enticingly put it to Amy Pond:
"So, all of time and space, everything that ever happened or ever will. Where do you want to start?"
There have been so many underlying plots within the hundreds of episodes - a Who-ception - that it becomes a source of fervent intrigue and fan theories.
Some get altered to fit a particular narrative arc. Some get used later on - the Zygon subplot from The Day of the Doctor eventually shapeshifting into a brilliant two-parter from series 9. Others are left as a sort of Hansel and Gretel breadcrumbs for other showrunners to perhaps pick up on, as Russell T Davies did with the mystery surrounding Peter Capaldi's incredible lookalikes throughout the Whoniverse.
Although some of the intriguing subplots on this list have been delved into in other media, they really should be further explored on the small screen (or silver screen!) given their blockbuster potential.