I'm not quite sure where the bad GK AI was in those videos. I have looked at all of the goals in those videos numerous times looking for trademark PES poor keeper AI and have failed to see it. What I saw was:
Atletico - Real Video:
1st Goal (Ronaldo) - Killer through-ball by Alonso (hopefully this isn't an issue again as it was in 2011) to an ELITE finisher. Keeper tries to come out and realizes he can't get to the ball. Ronaldo takes it on the 1-time. Ronaldo should finish this chance 9X out of 10. Maybe the keeper could have closed the angle but he would have easily gotten beaten near-post.
2nd goal (Mandzukic) - Perfectly placed low driven shot. Manduzkic on his strong foot with a great angle. Not only that but you have Pepe (who over-ran it) & Ramos (sticking out a leg) blocking Iker's line of sight:
Positionally, I thought Iker was OK and his slightly late dive could have been attributed to not seeing it.
3rd goal (Mandzukic) - sloppy giveaway by Marcelo stemming from the user trying to dribble out of trouble instead of clearing the danger. 1 pass from Raul Garcia and Mario is in on the keeper. Simple left-footed finish into the bottom corner. Not much Iker or any keeper could do when you give the ball away that close to goal. There simply isn't that much time to react.
I can live with all of those. What I saw was keepers coming off their lines quickly and aggressively, parrying the ball wide out of harms way and making all the saves they should be with the correct animations (one-handed dives instead of 2 when applicable).
I agree with you regarding the fouls though. I really wish PES would call more fouls when you're bumped/hit while kicking. There was a Mandzukic shot from the top of the box where he got hit, couldn't finish his animation, yet still got loads of power on the shot. That should have resulted in a foul AND a scuffed shot.