Although I'm not optimistic about Nunes, there have been quite a few players under Pep who have had pretty restricted minutes with limited success in their first season and have subsequently done a decent job.
Ake, Cancelo, Sane, Delph even Bernardo and Mahrez all made limited impressions at first.
Aké aside (because of injuries), the aforementioned players had already shown previously what they were capable of, & also showed their potential in flashes after we signed them.
With Nunes, I never saw what was the big deal about him at Sporting or Wolves. The first time he came to prominence imo, was Pep calling him one of the best players in the world, which made everyone sit up & take notice, but as we know, Pep says a lot of things.
Nunes always struck me as a panic buy after Paqueta fell through, & as others have said, Pep chose to bring on Stones against Ipswich to cover for a missing Rodri & injured Kovacic, rather than Matheus.
Bringing Nunes on at 4-1 up at home to a newly promoted side, with minutes of the match left, says a lot too.
I also reckon the Cancelo & Philips factor will come into City's thinking. Both players are proving difficult to shift, so City are probably taking the view that it's best to take a £10m loss & move Nunes on now at £40m, rather than keep him whilst he becomes harder to shift as his value decreases, whilst still taking up a squad place & slurping up £100k+ per week in wages.
A parting of the ways is best for City & Nunes. Sometimes in football, it's just the way the mop flops.