For one thing, the frequency of a word and the level of a kanji are different concepts. Any kindergartener who can't even write hiragana knows the word 誕生日 ("birthday"), and it's naturally classified as a JLPT N5 word. However, it has a rather difficult (and not very versatile) first kanji, and the kanji 誕 itself is supposed to be learned in the 6th grade.
According to this article and this article, the list of 教育漢字 by grade did not exist at first. The grade-by-grade list was introduced later out of concern for avoiding problems when students changed schools and textbooks in the middle of elementary school. There does not seem to have been any particularly detailed statistical consideration. Frequency was one of the factors, but the simplicity of a kanji shape was also considered. And that's why the grade-by-grade 教育漢字 list sometimes seems impractical to you. Japanese people naturally learn most of the JLPT N1 vocabulary before they turn 10, and even if they don't know many kanji, they have no trouble communicating. Even if they don't know the kanji 忙, the word いそがしい by itself is something they know from the age of 3. There may not be any particular reason to learn the kanji 矢 in the second grade, but there's no strong reason not to do so, either (its shape is simple, and it's frequent enough for an 8-year-old). If English is your native language, you have never bothered with level-specific vocabulary lists when learning English, have you?
The situation is different for a Japanese-as-a-second-language learner. If you want to acquire communication skills as quickly as possible, a practical vocabulary list by frequency and difficulty is essential. It's usually efficient to learn the word 忙しい along with its kanji. And JLPT levels are designed exactly for this purpose.