I've seen a few comments saying Natsume's Book of Friends doesn't deserve an S-rank. Personally, I haven't read it yet, but I think it's important to consider how different genres work before making that judgment.
You really can't compare popular shounen titles with something like Natsume's Book of Friends—they belong to completely different genres and target different audiences.
Shounen action manga usually gain more popularity because they're designed to be fast-paced, hype-driven, and appeal to a broader demographic. That doesn't automatically make them better. Many of the so-called "Big Three" are iconic but still have major plot holes and inconsistencies—yet they get S-rank ratings based on popularity and cultural impact.
On the other hand, Natsume's Book of Friends is a top-tier slice-of-life supernatural drama. It may not be as mainstream, but it excels within its genre: beautiful storytelling, emotional depth, and character growth with barely any plot issues. Just because it doesn't have flashy fights or massive hype doesn't mean it deserves anything less than an S-rank.
[p.s. :- I just looked it up and read through a bunch of reviews and reactions. It really seems like something special in its genre.]
Every genre has its masterpieces. A work should be judged within the context of its genre, not just by how many people are talking about it.