I love this new system, and I am 100% sure that big clubs will end up trying to make some changes on this new system because of what happened as well. Look at it, Real Madrid is 20th, and thanks to their latest win, they could have been literally out of top 24 if they didn't get this win.
Manchester City is 22nd, they are literally just barely in, and this is the team that did treble one and a half season ago, and now they are looking like they may literally miss their chance. Don't get me started on PSG, they are literally 25th and out of top 24 right now, sure they still have a chance to get back in, but that is just so weak. Not every big team is doing badly, but these big teams are definitely not looking good at all.
Many big clubs have not been able to adapt to the new system. the clubs you mentioned, one of which was not been able to adapt it. Many their player injured because the new system, and another club not yet familiar with tight schedule.
Those big clubs were not fully preparing. They're kinda stupid when they were not adding more players to their squad, and think to complete the longer season with their available squad. Their stubborness makes their players faced a higher injury risk due to the busy schedule. They should have copied what Chelsea has done to have at least 2 squad in the same club.
The new system has forced the club to milk their players to play even longer than what they did usually. It makes their players have to put more efforts in order to play in any competitions. This is really burdenting their stamina, phisic and morale.
Manchester City was drop before the time, they will most likely overtake Girona on the bottom board because they don't have been able to adaption the new system, this was once expressed by Pep in the interview session that the new system makes their players tired, and easy to get injured. he hopes this new system will not be continued for next season, and come back to old system.
It's pep's fault for not even aware about how intensive their schedule this season. Also, some of his players are injury prone as well. It's wrong if he blames the new system.