The issue of 3-5-2 or 5-3-2 however you want to look at probably won't fix itself when Mendy comes back.
Firstly I will qualify that statement by saying we will definitely have more balance and in turn just by maintaining width on that side of the pitch, the guys in the middle will have more space and time. However our big problem is two fold. Firstly, Fernandinho, despite being all action and receiving praise from Pep (probably more so for doing a job that he isn't suited to) is a problem as the pivot and as the holder. As the pivot, he's not quick enough at breaking the lines with forward passes. This delay or hesitation is that difference between an attacker receiving the ball on the turn and an attacker receiving the ball heavily marked with his back to goal. As the holder, he also isn't disciplined enough to hold his position and not gamble and winning the types of 50-50's that look great when they come off, but land us in trouble when they don't. Our backline would be more effective if we had a holder who could delay attacks rather than attempt to stop attacks with an interception. This would have an added benefit of us being able to invite teams on to us a little bit as well, which gives us more space if and when they turn the ball over.
The other issue lies with our backline's options when they have the ball. The wing backs push up and wide, but are heavily marked so their pace is totally negated. Because they have pushed wide, KDB, Silva, Kun and Gabby tend to sit narrower which means their first touch has to be spot on if a ball is played forward. This isn't always the case and when it's not, our play becomes totally fragmented.
One fix for this issue is for Pep do invert the wingbacks but only when our three centre backs have the ball. They could both act as extra pivots in the centre, and when they invert, two of the remaining four attackers could offer width until we have advanced the ball into the final third...at which point they can revert to their initial position. Pep did this at Bayern to great success. He even did against us iirc. My only worry would lie in Mendy and Walkers ability to receive the ball on the pivot, although if they were 1 of 3 options, they would probably have enough time to pivot without being under too much pressure.
I tend to feel that good teams will just man mark the one pivot we use (currently dinho) and stop him from breaking the lines and advancing the ball forward into dangerous areas. The width that Walker and even Sane offer as wing backs is totally false width as they are receiving the ball whilst they are stood still almost, with no other option other than to go back to the centre backs.
Another issue causing our play to appear fragmented lies in the opponents ability to use the channels against us. Clever teams will continue to employ pacey players in the channels in an attempt to get up the pitch. This will mean that they counter with more regularity as they have a fairly simple out ball. We couldn't build enough momentum at times on Monday because Calvert Lewin worked the channels so well so their counter attacks lasted longer than they should...particularly if we gave a foul away out wide. This tended to happen quite a lot and it totally broke the game up and when added to the issues already mentioned, it meant that Silva and KDB both tended to drift out of the game....and once those players drift out, their touch becomes less reliable and their influence less productive.