I think it's different because she's a side character. She's more part of Mario Galaxy's background story than an active role.Which if it was fan fiction, would be seen as laughably stupid and over the top. But no, because it's a published game, it's 'interesting' and 'meaningful' and 'deep'.
I personally liked her in Galaxy. I think it's creative how she raises the source of all the the universe's suns, moons, planets etc. from birth to adulthood instead of just magic-ing them into existence like most portrayals of a God/Gods.
It bothers me more that she went from a literal deity to just another one of Mario's pals who shows up in everything and can now die for some reason.
I'm not gonna argue whether she's "deep" or anything but I do think that her storybook backstory was very touching and that in Galaxy 1 she was very graceful and majestic and that her overall presentation was really beautiful. That made the whole deity thing a lot more believable.
Right from the start it's apparent that she's no normal human being. But they also didn't shove it in your face like "I AM GOD. ACCEPT IT!"
The whole thing was a lot more subtle and believable than some fanfic.