I'm a little torn on this. On the one hand, I agree with the sentiment that just because it's Mario and it's mainly for kids, that shouldn't mean that the story doesn't matter much as long as it's fun. The best and most beloved animated films are exactly those that also incorporate heartfelt emotions and put a lot of thought and heart into the story and its themes, while ALSO being fun to watch.
On the other hand, I also don't think "just being fun" automatically makes a movie (or tv show) mediocre or bad. I can think of plenty of examples where the story isn't very deep and the movie doesn't attempt at all to tell a deeply engaging or moving story, but just focuses on giving you 90 minutes or two hours of pure fun and entertainment...and I don't think there is anything wrong with that at all. I don't really like the idea of sticking up your nose at something because it's just fun and meant to entertain people, as if that has no value in of itself.
Plus, the "It's Mario, what did you expect?" argument has some validity imo, because the appeal of the franchise certainly never was its deep storytelling. So it does feel a little disingenious to me to complain about the lack of depth in the adaptation. Not that they couldn't have tried to do that, but I wouldn't exactly call it mandatory to create a fitting and pleasing movie adaptation of the Mario franchise. Things would be different with a movie adaptation of, for example, the Zelda or Metroid franchises, i. e. game series with deep lore, more mature themes etc.