I agree that he has a lot of utility. If he was 100% committed to SS, he probably could be better than Story. Switching between the two positions is not helping him in the least.
The problem remains where to put him while you have Duran and Story on the roster. 2b is a waste. I think they need to decide where they want him for the next 6 years and just put him there on Opening Day. From what I know of the Red Sox, they'll continue to hem and haw over the decision and he'll still play all 3 positions in some manner next season UNLESS they deal a few of the playing time roadblocks.