The ambiguous pronounciation of kanji in Japanese language comes from the fact that it was imported. The characters were imported along with the pronounciation in China at that time. The characteres were imported three or more times and there exist more than three ways to pronounce the word. Sounds ridiculous but there still are ways to pronounce each kanji. The funniest thing is that the revolutionary idea of formulating a way to pronounce kanji is actually rejected because that kind of system benefit those who are not properly educated to read kanji. I believe, to standarize the use of the language is one of the one of the most important task of liguists and the educated.
It is fantastic thing to be able to read kanji. One can read without pronouncing them. This flexibility is one of the reason why the pronounciation is not standarized.