I think you hit several nails very firmly on the head here. This morning I read Pep's comments on the games and thought I must be his ventriloquist's dummy because he explained the difficulties of managing the best team in the world with a clarity that I certainly can't match, but then he is actually managing the best team in the world.
City have had to play 5 games in the last 14 days. We played 5 in the 3 weeks before that and 6 in the 3 weeks before that and so on. What marks the 5 matches played so far in April out is that they are in 3 different competitions and leaving aside Burnley were 2 against Liverpool and 2 against Atletico, one of which was a brutal and bruising encounter. Defeat in any would have disastrous consequences and Pep picked the best team he possibly could for the home and away legs against Madrid and the home game against Liverpool. It has to be pointed out that games against Liverpool are always high intensity, draining games and the game in Madrid left Walker and KdB unfit to play on Saturday and those who played in the previous games too drained to meet the physical demands of a sudden death game against Liverpool at Wembley. Pep had to rotate, though his options were limited: only 3 players who had not played at all in Madrid played yesterday and these 3 had all played 90 minutes at home to Liverpool and in the case of Phil Foden he had been singled out for particularly violent attention in Madrid. The three players you name are indeed good players but are not first choice and the team is weaker with them in.
Liverpool had not had the problems we had. Indeed 7 of their high profile players had a week off before the semi. Our experience is that against Liverpool the first 25 minutes see them playing at very high intensity and trying to press the life out of the opposition; weather this storm and you seize the initiative. Yesterday their fresh players pressed a team which understandably was a yard at least off the pace and just as slow in thought - the set up was ideal for Klopp's gegenpress and it worked well. City couldn't play through it and the legs in midfield were too weary to play through it. We improved greatly in the second half but we were never our real selves.
I would say that if we had to lose a game yesterday's would be the one I'd choose. Pep would be horrified at that and tell us all that he picked the best team he could in the circumstances and, of coure it goes without saying, he's right.