Still no idea who Mrs. Flood is, except the obvious answer would be The Master, considering what she said earlier in the episode. It did occur to me that she could be some incarnation of River Song.
Ruby's mother ... when I saw the cloak she had on, I couldn't get the outfit Jodie Whittaker had in the trailer that announced she was the new Doctor out of my head. Still not much clue as to who she could be, except that maybe that figure will turn out not to be her mother at all.
"The one who waits" is presumably Sutek (presumably also the "Boss" who the Meep referred to) - I'm unclear if Susan Triad was really Sutek all along, or just being used as an unwilling vessel. I can't get over the fact that I missed her being Lindy's mum two episodes ago.
The Doctor mentioned "Time changing", like the whole "Mavity" thing from the Tennant episodes, and certainly seems to have been a recurring theme. So, it could be that parallel universes will come into play, or someone just making subtle changes to history, like the whole butterfly bit in episode 1. It could even explain Susan Triad's many guises.