People are confusing ability on the ball with passing ability.
Stones isn't a phenomenal passer, he's a good passer, accurate, and can pass his way out of trouble but he's not going to hit through balls for aguero or 50 yard diagonals.
What he's exceptional at is beating defenders and moving into midfield, creating forward impetus and putting the opposition on the back foot. He's beaten more defenders than any other centre back in Europe this season. It's that quality which Pep values so highly in his centre-backs, and why he's used midfielders there in the past. Get past the first defender, get the opposition out of shape, create forward momentum.
Also I'm not sure why anyone would expect a player like Yaya not to drop deep for the ball? Guardiola's teams have always had defensive midfielders who drop between the centre-backs, about as deep as it's possible, and it's been the same as long as he's been here as well.