The old official system arguably makes more sense from a Japanese perspective.

If you look at the kana, the Japanese syllabic writing system, they have this ordering: ka ki ku ke ko, sa shi su se so, ta chi tsu te to, etc. If you follow the regularity where there should be a "ti" sound there is no "ti" sound and it happens to be pronounced "chi".

One common analysis holds that the underlying phonemes really are: ta ti tu te to. Traditional Japanese grammarians usually analyzed it this way. And they were historically pronounced that way: it has arisen out of relatively recent sound change. Somewhat like how some British speakers pronounce "Tuesday" such that it sounds much like "Chews-day" to speakers of other dialects. Affrication in a fixed context. The t phoneme triggers that kind of affrication obligatorily in Japanese, before the i vowel or y glide.

Some disagree with this as overly theoretic and based excessively on historical linguistics, and they insist that sh and f and ch are distinct phonemes in Japanese. But the Japanese writing system itself treats it as if they were not.

If you are learning Japanese it makes sense to pick a system that reflects the internal logic of kana spelling. If you want to just approximately pronounce Japanese words in English then you want something that reflects the logic of English spelling.

These two goals are always in tension. Mandarin pinyin, for example, was designed to reflect the logic of Mandarin phonology in a consistent way. It's not meant to be easily pronounceable by English speakers. It's to enable Mandarin speakers to look up words in a dictionary or for students of the language to study Mandarin. Though it has ended up used as a pronunciation guide for English speakers. And that often doesn't go well; a lot of English speakers don't know what to do with the q's and x's.