Sorry to go all generalist in this comment, and happy if this post gets relegated if I stray too far but...
I am so fond of the longer Dr Who story arcs and the gentlemen guiding the show have shown themselves rather good at stitching disparate points together over a period of time to create unexpected and satisfying denouements. This is particularly the case when it comes to the seemingly unreliable finality of death.
The clues in plain sight, and the things that we are expected to accept and then slap our foreheads at in retrospect, are now the tradecraft when it comes to this kind of tv. The old rules of a whodunnit have been expanded to touch on central characters (as opposed to guest stars) and stretch across seasons (as opposed to within episodes) and to play with themes and boundaries that writers were not free to cross on TV in the previous century.
What it means is that television now bears far greater scrutiny than ever before, and at the same time affords us the tools to do so.
So now, as a staunch "Moriarty's Game" theorist (based on what this episode has shown us), I am now inclined to head back through the catalogue and see what a closer examination of his appearances and references might yield.
I'm sure there is a thread for this. I shall seek it out and post more there.