Interesting but I think the two Naughty Dog examples are quite poor. Chloe in Uncharted more obviously so as she, along with the other main female characters throughout the series, are always shown as equally adept as the main character in combat and traversal. If the sole issue is her complementing the character then that's a bit odd since the male characters in the series do the same thing too. I have no issue with the women shouting 'good shot!' or whatever, if they're portrayed as equally competent. As she says in the video, it's simply positive reinforcement regardless of gender.
I also don't have a problem with Ellie in The Last Of Us. For starters, she's a young girl who has very little experience of the world outside where she grew up, which is why she can't swim. It's essential to the plot that she and Joel not only have to develop a bond but also that the bond is one resembling a father/daughter relationship, one in which Joel feels compelled to protect her.
It would be far more incongruous if a young girl was suddenly thrust into the world able to swim and wield guns adeptly, and it would probably be detrimental to the story arc. Regardless of Joel having to help her across water or up ladders, she is shown as smart, capable and the tables turn when she has to look after herself and take care of Joel later in the game.
I do enjoy the tropes videos but occasionally they do have a tendency to rob things of their complete context in order to make a quick point.