Komugi might be a odd variation of the "innocent Mary Sue" trope, yet I feel her character is just right for the story as is, particularly as her self-esteem issues are treated realistically and she serves as a perfect foil and compliment to Meruem. For the peak of evolution, the natural-born king to find his peer and opposite in a disabled, unassuming girl is pretty great IMO, and it sets the stage for both of their characters' growth.

The development of their relationship and eventual death hits just right for so many reasons well beyond the trope IMO. It's honestly very perfect and I would describe their dynamic as not unlike the "shonen male friendship" described in the post- they grow with each other (though Meruem gets more character development), they complete each other, and they choose one another- perhaps with the difference being that choice is maybe as far from destiny as it gets- at the end.