Gradings are subjective; there’s no escaping that. Even those who attend the same classes, use the same learning materials, and spend the same time studying will have differing opinions on how difficult something is. Natively uses the wisdom of the crowd to gauge difficulty, so the more people contribute, the more accurate the level. It’s not a rigorous academic study where you can control who reads what.
Who’s to say how difficult something “really” is? Everyone (including you) is judging by their own perception of how difficult it felt to them. You can take different aspects of the language into consideration, but this doesn’t negate the fact that it’s subjective.
Visual storytelling helps provide context, which naturally aids understanding; should those who read novels disregard the plot because the natural patterns found in narratives give contextual clues that help with understanding the language?
This is your opinion - there is no objective measurement of difficulty that makes you right and others wrong.
Are you proposing that only advanced learners be allowed to grade items? Then exceptionally few items suitable for beginners and intermediate would have gradings at all, not to mention you’d be excluding the people who could actually give feedback on whether or not something is suitable for the level that they are at.
You could make a whole list of things you think people should or shouldn’t take into account when grading, but it’s hardly as if you could enforce this. You could make a rule that only those who provide proof of having passed the JLPT N1 are allowed to grade items, but then there would be very few items graded, most of which would only be graded by one person. And how would you be able to tell if they’ve judged it well? How would you know they even read the book at all? I could go on, but you get the idea.
While I can agree on some of the issues you raise (I think Detailed language evaluations would be immensely useful for providing more information about what makes something difficult), I think a lot of what you’re unhappy with just stems from the subjectivity of grading, which is not something that’s going to change - everyone has different learning methods, experiences, and opinions, and this affects how they grade item difficulty.
Rather than being a flaw, I think it’s more beneficial to have a wide variety of experiences, especially if people include reviews - it makes the grading result more accurate and is helpful to more people. You could have an expert draft a list of media in order of difficulty according to their professional opinion, or have students taking the same class all read and grade the same items, or even create something similar to JPDB that takes more than just vocabulary into account… But none of these would be able to produce objective difficulty levels, either. And they certainly wouldn’t provide the volume of information that Natively does - over 12k Japanese books have non-temporary ratings.
One last thought: Natively is merely a helpful guide, it isn’t claiming to be a definitive source of the objective difficulty of foreign-language media. Difficulty levels fluctuate, and people can disagree with the level of even the most graded items, but that doesn’t detract from how useful it can be for finding things to enjoy at whatever level you are at in the language you are studying.