I have been very consistent this season in saying I think our biggest problem has been a lack of pace and natural width, caused by Sane's injury and subsequent departure.
Personally I think Pep knows the problem, hence why Torres was our first signing.
However Pep's hands have been tied this season. The lack of pace and natural width have meant we have had no option but to play centrally more frequently, which teams have realised and exploited by packing central areas and catching us in possession, which has lead to numerous goals conceded on the break. To try and minimise that vulnerability Pep has gone for technical superiority in midfield, which has resulted in some teams physically dismantling us and giving us a bit of a slap.
People blame the defence and CB's in particular but they're being left exposed by a drive for technical superiority rather than a technical/physical balance in midfield. Gundogan, Rodri and Silva (Fernandinho, Mahrez, Mendy and Aguero all exaggerate the problems too) are all limited physically and cause our defence untold problems when played together.
A few new signings to give us the pace and width back will fix the defensive problems as well, as teams won't be able to defend narrow and deep against us. They won't be winning the ball in central areas as frequently meaning they won't have as many counter attacks, so our defence will be less exposed as a result.