To be fair both Stones and Otamendi looked dodgy during that time.
I would agree that is the main difference, you look a lot more open in midfield without Fernandinho in there.
They looked dodgy because even then at times they were forced to defend 2 vs 2 or 2 vs 3. It happened a couple of times a game and led to a mistake maybe 1 in 5 games. This season the lack of cover exposes them 5-6 times a game so they look far worse. I still believe you slap two or one good CDM who actually does the job in front of Otamendi and he's ok. Not a great defender by any stretch but their is cover for when he does dive it.
Its no coincidence we've only taken 1 point from 7 games vs Spurs, United, Liverpool and Wolves (all teams who defended deep even Liverpool) got the ball and went clean through our midfield like they were asleep. Again I'm not saying Otamendi is world class, I'm saying he's decent if he gets a bit of help. He defends on the edge because of a lack of pace though. He was in the team of the season 2 years ago. Stones is a problem, he hasn't improved at all defensively and is still a bottom half of the table centre back, after Pep he'll end up at West Ham or something.
To make a comparison look at what the return to form from Matic has done for Maguire and Lindelof. They were getting slated on here till he got back in the team, all of a sudden they are doing well and United aren't conceding because they have protection and cover.
Pep teams in general are always going to expose defenders, even Pique used to get slaughtered as being "good with the ball and poor at actually defending". Something he has since put to bed, its a common theme. I still think we'll bin Otamendi end of season but I fully expect him to do well wherever he goes.