The main problem here is not the manga's structure, but people not getting said structure. If you go in with the assumption it will follow the "main pair" as the central driving plot you just misunderstand the point. Shiramine and Kurosawa are the framing device that holds the narrative together, but ultimately it is a story that follows relationships at the academy.
I'd argue that not being able to follow the plot is not because I'm stupid but it's because the author didn't even try to make it clear. If for example there was a clear pattern like one chapter of a volume about the main couple and the rest of the chapters are about the other main couples or if the chapters about the other main couples would be side chapters like in comprehensive tovarish.
This doesn't read like one plot this story reads like a compilation of short stories with an excuse to link them together.
Also because of the huge focus on side characters the allegedly main couple didn't get enough development in my opinion.
Oh my, never expected a response to that months later. Glad I wrote it then.
So first of all, it was not my intention to call anyone stupid. The structure is unusual and many people will inadvertently go in with set expectations of what a romance manga should be. Sometimes preconceived notions blind us to unexpected things. The structure of this manga is not at all confusing in my opinion, just unexpected. Many people don't get how it works or why it is done this way.
You sort of already got the structure you are asking for in your comment. Every volume tends to have one chapter that focuses on Shiramine and Kurosawa's relationship at the minimum. In fact that is the one ironclad rule in this manga. They are the connective tissue so that it does not feel like an anthology and the reader can tell that progress is being made and time advances. In many cases Shiramine and Kurosawa are actively involved in the other pairings plots, sometimes with a very minor role, sometimes with a larger role. Their presence never disappears completely.
I find it regrettable that you think the main pair did not get enough development, but I don't really think that can be objectively pinned down anyway. To me their arc is very fulfilling and believable. The final chapters and the slow build up to Shiramine's realization were very well done. I am truly confounded that some people called it rushed. Then again, other people called it a slow burn, so you can't really satisfy everyone either way.