Difference is the starting point. The City Pep project started well before Pep joined the club with some backroom people from Barca moving to City to set up the club, buying certain players, employing certain coaches and scouts all to help Oep have a soft landing. In comparison, Jose came to a club that had significant strategic issues with a split dressing room, a total overhaul of the playing system and 6 poor transfer windows.
Comparing the two on this season alone, I think Jose is doing the better job despite the relative league positions. His purchases have had more impact and despite having more to do and starting from a weaker position he has delivered some good results and a degree of consistency that we have lacked in the last 3 years. Pep started really well but like Klopp has hit problems once teams have worked out his system. City and Liverpool do not seem to have a plan B and Utd have a few alternative playing styles. If you take Thursday, Jose played it perfectly recognising that Rostov would blitz in the last 1/3 of the game so he played it safe and waited for them to open up.
So Pep has underperformed based on coming to a club that was, in part, set up for him.
Next season will be career defining for Pep and Jose.