I tend to take whatever order that person would use when it comes to the name, so Japanese characters get the family name/given name order. If there were any westerners on the chart, the name would have been reversed for them. And diacritical marks tend to make things harder to type and harder to read. The pronounciations might be more accurate, but the doubled up vowels are pretty close, especially if you're somewhat familiar with the hiragana set to begin with.
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