It's a fair point, but a pretty niche one - I expect that the overwhelming majority of foreign-language pinyin users are learning standard Mandarin. If you're learning Min or Wu as a second language, you've got bigger problems than the quirks of your transliteration scheme.

For native users of pinyin, the consistency with English pronunciation is essentially irrelevant.

Sorry, I didn't make myself clear and also for belaboring the point. I wasn't referring to separate dialects, but local non northern mandarin which gets pronounced slightly differently than received pronunciation.

A brief example, yes/is, approx [shi], might be pronounced approx [si], etc. But it's mandarin and not hakka, min, etc.