This is a thing I think about pretty often, and I’ll come up with some of my own examples to start.
Reading. I played Link’s Awakening*when I was 4 years old, and while it wasn’t what taught me how to read (I started reading when I was about two and a half years old), it certainly advanced it, considering how writing-heavy it would be for a kid at that age. Pokemon and Harvest Moon 64 probably helped as well.
Map Reading and Directions. There are so many maps in games that a certain point it makes sense that you’d start to pick up on reading them efficiently. I’m able to draw maps in my head and visualize where to turn and things like that, and I think part of that has to do with always knowing where you are. Dark Souls, funnily enough, helps the same way, but with its lack of maps.
Personability. More of a soft skill, but Persona 4 made a big impact on how I approach situations with other people. I’ve become someone who says yes to things, whereas before I was much more withdrawn.