It appears that many native Japanese speakers have the same reaction to much that is taught here. (My wife also made similar comments.)
“What?! No, that’s wrong! Why on earth would you teach unusual/obscure word instead of common word? Why is that taught before that?!” Etc.
True experts are often, usually even, the worst teachers. They know all the exceptions, all the nuances, all the confusing factors. They sometimes find it painful to over-simplify in an attempt to teach the basics of something. They worry about precision and factual truth more than pedagogy.
It reminds me of something I read a long time ago. (I think, but I’m not sure that it was in the book “The Science of Discworld” if there any other Terry Pratchett fans here.)
The author discussed “lies we tell children”. The answers to “Why is grass green?” and “What causes rainbows?” are incredibly, outrageously, ridiculously complicated. Very few adults really know the real answers (I certainly don’t) so we just mutter vague hand-wavy things (maybe even mentioning chlorophyll, moisture-induced diffraction and other things that we don’t really understand).
By teaching a “lie” (an oversimplification) the student understands just enough to make progress. They either lose interest, or they start asking better questions and finding better answers, eventually drilling down to “truth”.
Wanikani won’t make us expert linguists. We won’t achieve a deep understanding of Japanese, but it demonstrably provides enough of a basis for we “children” to learn enough to start asking better questions and better understand the answers.