People misunderstood the type of player he is, myself included.
Pjanic is a great passer, and playmaker. He is also very technical with flair. He is also weak on the ball, and generally doesn't like holding onto the ball for the long periods of time. This makes him no regista. He is a good passing outlet, but he needs someone else in the midfield who is capable of holding onto the ball and running with it. Pjanic will give him passing outlets, and make nice flicks/ long range passes, but he will never be a water carrier.
He is effective, but with Marchisio and Khedira, I'm not sure we have the legs in that midfield, especially if Marchisio is playing in a deep position. Marchisio 3-4 years ago would have been the legs, but post injury and with age, I'm not sure if he is most effective in a box to box position anymore. If Marchisio remains the water carrier, the RCM position needs to be filled by someone with legs and technical ability.
One possibility could be allowing Hernanes to play as the water carrier and if Marchisio is fit enough, deploying beside Pjanic.