I think Pep was thinking about the big picture including possible games against Bayern and PSG, and not just about Lyon. And that wasn't a mistake either. Why?
Because we can't play with high pressing and intensity every 4 days. Against Real we covered 112km and made a lot of sprints. We can't play 3 games like the one vs Madrid over just 10 days.
To beat Lyon and stand a chance against Bayern and then PSG, we had to be as fresh as possible, especially given that both Bayern and PSG/Leipzig have more rest than us.
That's one of the reasons why Pep tried a more economical way to play and beat Lyon, in order to have legs and stand a chance against Bayern. It was obvious to the eye that we played with less intensity than against Real.
That was a calculated risk but it backfired because of individual mistakes on our part and VAR. Truth is VAR was decisive for the outcome, not just our performance.
So, I tend to be less critical of Pep now than after the game. The objective wasn't just to beat Lyon but to beat them in a manner that gives us the best chance to win the tournament. Management of resources was necessary. Still, Pep should have made changes earlier and sub not just Ferna but also one from Rodri/Gundy and bring on Foden and Bernardo.
Hindsight is easy though. Pep's just human. I'm grateful for what he has done for City. Centurions and domestic treble winners: feats that have never been achieved before and might not get emulated soon as well.