Avoiding Human Exceptionalism does not mean making humans weak and dumb, this is completely missing the point. My issue is when humans kick ass due to "being human", as opposed when humans use some reasonable advantage that they may very well have to solve problems they face. How it comes across depends on the quality/style/context of writing. Some works can sucessfully characterise humans as having legitimate advantages without making it seem like we are somehow magical. I would think it has to do with how abstract human advantages are. Something like "Human Nature" is very vague, and tends to play on our emotions.
Take American Exceptionalism for example. America has a large economy and heavily influenced the world throughout the 20th century. But you can seperate that from "American Exceptionalism", the idea America has a large economy and strong influence merely
because they are America.
It can lead to the idea that they cant fail too. "America cant fail because we are a God-given gift to the world", "Human nature will always save Humanity (somehow) in the end".
Unless it's a weird artsy videogame, games are around to make the player feel powerful, so if the player character is human, then humans (or Americans, or ninjas, or whatever group) is going to be the dominant force in the setting. Who would want to play a Pokemon game if Pokemon were just regular animals that looked funny?
It has nothing to do with being a dominant force in the settings and everything to do with
how they are a dominant force in the setting.
Interestingly enough, Ninjas is one thing that media often treats as some magical, mystical thing and the common representation of them often falls under Exceptionalism. Are the Ninjas powerful
because they are Ninjas (i.e. they are Exceptional)? Or are they powerful because they spent years training and practicing, and they use their training to their advantage (a perfectly reasonable advantage)? Not being exceptional does not imply not being strong. There is no reason why humans cant save the universe, but it gets obnoxious when all the
Other species can't because simply
because they are not human. Also note here, the player is a
Human, but the player is not
Humanity.
Games are not necessarily around to make the player feel powerful. Have you ever felt powerful playing something like Ski Free? I can't think of any reason why games have to make the player feel strong. Why is "weird artsy games" dismissively applied to all games which dont make the player feel powerful?
I should also point out that Human Exceptionalism doesn't make a piece of media objectively bad, I just find it blatently patriotic (particularly in video games) and I find patriotism to be obnoxious.