Asking about why something took so long to happen in a show about time-travel is perhaps a little silly, no? We all know by now that time doesn't travel in straight lines in the Whoniverse. Possibly Sutekh was waiting for a Doctor who was more likely to fall for hs plan? It's not uncommon for the Doctor to be blindsided, but usually in ways that relate to their current personality. This one is more emotional, less detached, than most of his predecessors for instance.

In the matter of Rubys' mother, there is no guarantee that it was her who took Ruby to the church - even if she recalls doing so. The fact that Mrs Flood made her last enigmatic announcement in a snowy scene indicates that Rubys' arc is far from complete.

There was something about Ruby and her origins that bothered Sutekh. The Doctors' pat explanation leaves too many questions unanswered.

What was it River Song used to say? "Rule Number One: The Doctor lies!"