I'd have started Otamendi personally. I agree though, it's the end of their careers at City unless there's a dramatic change of heart from Pep. A 19 year old kid who wants to go to Barca getting picked though? Something is seriously, seriously wrong behind the scenes.
It's worth saying that in 16/17 Pep made every effort not to use Zabaleta. Hart and Mangala were sent away at the first opportunity. It was known that he wasn't a big fan of Clichy or Sagna either, particularly with the latters injury problems. And only rated Kolarov as a CB. He played Navas and Fernandinho as fullbacks if he could get away with it. He also abstained from using Touré for the first half of the season, and barely used Fernando in the second half of it. The season after Touré barely featured. The season after Delph was effectively banished after he got a red card. As this season has gone on, he's used Silva, Otamendi, and Stones less and less. Bernardo has found himself marginalised. Mahrez has been slowly pushed aside too as the season closed. Zinchenko has effectively disappeared.
It's probably not a coincidence either that he only used 2 subs against Lyon, even if it was wrong to do so.
I'd wager with Pep that if he doesn't see value in you at the time of asking, you don't play unless you have to. He's VERY ruthless like that. Probably too much so. There are some players he loves (as players, not people to be clear), and they always play: Sterling, De Bruyne, Walker, Ederson, Rodri, Laporte. And then there are the players he likes, the ones he'll happily play but maybe doesn't think the world of them, at least right now (due to being young, due to being old, due to not quite being the right level of quality but showing all the other good signs etc): Fernandinho, Silva, Aguero, Jesus, Gundogan, Mendy, Foden, Garcia, Mahrez, Bravo. And then there's everyone else; I'm playing you because I have to or you have a specific skillset that could come in handy. The fact I feel Bernardo is here is a concern. It's worth adding here that until Cancelo improved his attitude after the lockdown period he wasn't being used much either.
We're not seeing it publicly but I'd wager there are a lot of players Pep is absolutely livid with at the moment. Some he wants nothing to do with and some that he thinks seriously need to get their acts together. I think the club know that and that's why we're making big moves in the summer market. But that's why we're seeing certain players uninvolved even though they maybe ought to be.