My personal theory is it was because of hiatuses and competition!
- Hiatuses: Sherlock especially, but the long Doctor Who mid-season breaks didn’t help. People wandered off. Some of them to very similar shows, like Elementary, which fought initial fan scepticism to become THE Sherlock alternative.
- Fans became more critical. All three shows frequently come under fire for their treatment of women, LGBTQIA people, etc., and without new content fans had no option but to rewatch and reexamine the same episodes over and over again. Their flaws became more obvious on repeat viewings, and the comparison to new arrivals like Elementary didn’t help. I imagine there were other competitors too, but one would need to do more research to see how relevant they are here - cartoons like Steven Universe and Gravity Falls, maybe? WtNV? OUAT and OITNB? All of them are much more obviously diverse, so Superwholock starts looking bland in comparison. There’s also the quality-comparison argument (Doctor Who is not as good at plotting as a lot of other things), but I reckon that goes without saying.
- Fandom backlash! You either die a hero or live long enough to become a villain. After events like the Mishapocalypse and the infamous FANDOMS GRAB YOUR WEAPONS post Superwholock became shorthand for the most obnoxious parts of Tumblr and fandom, so more people starting distancing themselves from it (see also: how Bronies killed the MLP fandom). And, yeah, it all came to a head with the Dashcon Clusterfuck 2k14.
- Fandom Backlash II: Your Fave is Problematic. Every popular figure from Joss Whedon to Taylor Swift is eventually the subject of text posts and screencaps dragging their name through the mud. Steven Moffat, Benedict Cumberbatch, Martin Freeman, and Jensen Ackles (I believe? It might have been Jared Padalecki. I don’t really follow Supernatural) have all had plenty of this.
IN CONCLUSION: there wasn’t enough new stuff being made. People found their own new stuff, which in many cases they found more appealling. People became less forgiving of the old stuff, its creators, and its fans. Eventually enough time passed that they gave up on the old stuff completely, so when it came back they weren’t interested.
(granted this mostly comes under the seasonal rot and kids getting older points but I didn’t notice that until I’d typed this out, and it seems a waste to delete it now :P )