This is one of those shows and they do it well.
Convoluted plot? Superhuman abilities that defy belief? A lore reason to wear schoolgirl outfits? Convenient resolutions without convincing explanations? Doesn't matter. None of it matters. There could have been aliens that worship a flan god beneath a mountain made of mochi and it wouldn't have mattered. This is among the group that sits at the zenith of cute girls doing cute things and all other concerns take a back seat to that. Chisato is far too likeable as a main character for a measly nothing such as plausibility to get in the way, and her relationship with Takina is so endearing it makes you want to squeeze a stress ball. Everything else just adds flavor to that.
It's also well put together. This show really could have been about anything. The fact that we got government trained adolescent female assassins that fight terrorists/criminals while running a popular dessert shop on the side pretty much says it all. Compared to this, a tragedy, romcom, horror, or anything else is easy by comparison.