The Cultural Affairs Agency has finalized a draft proposal to adopt the Hepburn style as the unified standard of romaji, or romanized Japanese, primarily due its closer resemblance to English pronunciation.
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Currently, schools [in Japan] primarily teach the kunrei style in accordance with the existing Cabinet announcement. However, the Hepburn style is widely used in society.
using romaji as a guide to pronounce is problematic no matter what system. pronouncing strictly based on kana is not problem free either. Korean hangul romanization may be a more obvious example of the dissonance with pronunciation but Japanese also has it.
most effective is to rely primarily on listening.
having grown up in US, I can say that our English instruction for anglophone natives draws a false equivalence between pronunciation and orthography/spelling. this creates a counterproductive mindset for approaching new languages.