Aguero's decline as a player started already in 2018. He was still a top, top striker in home games (scored vital goals in big games at the Etihad, especially that goal vs Liverpool in January 2019 was absolutely fantastic), but he was a bit ordinary away from home after 17/18 and especially after 18/19. Pep must have known Kun wasn't good enough to start big games away from home (that's why he benched him vs Real), but he continued to play him in the PL (Kun started most big games away from home in 19/20 and did nothing in them). I guess Pep didn't want to rock the boat back then.
Aguero and Fernandinho were a bit too old to rely on them to turn things around in the CL final. In hindsight, Torres and Rodri would have been better options, because they are big lads and could have helped with their physical presence in the box in the final 10-20 minutes. Pep probably preferred better leadership on the pitch over more physicality: that was probably a wrong decision, though. Our biggest problem in the CL final was that we couldn't match Chelsea's physicality. We got better when Jesus was subbed in, and could have been even better with Rodri and Torres instead of Ferna and Kun. But imagine the criticisms had Pep subbed in Rodri and Torres instead of Ferna and Kun and City still lost the game!