I disagree..... I think that it is simply that some of his decision making is poor at the moment. I also think that he was over confident on many occasions last season and tried to do too much on the ball.
Some of Stones' defending was excellent, but he undid his good work by making some horrific mistakes. I think as he takes on board good coaching, gains experience and starts to take the right option more often his overall performances will improve greatly.
Stones has the right physical attributes to play centre half, he is quick enough, good on the ball, has excellent vision, passes well and is generally positionally good for a player of his age. The reason that several of the top clubs want him (and Everton resisted big bids for him last year) are that coaches can see that he should develop into a brilliant central defender. The potential ceiling for Stones as a centre half is huge, that is why Chelsea and Emirates Marketing Project are prepared to gamble big money on him now.