Comment by efskap
Plus, a more phonetic writing system is also problematic for dialectal variation. I pronounce marry/Mary/merry identically, as well as bag/beg, but other dialects distinguish them. I don't think the written standard would benefit from spelling them identically. That's relevant for everyday use, not just upsetting etymology enthusiasts.
Of course it also depends on how conservative the language is, like Finnish orthography is practically IPA, and yet Finnish is a freaking time capsule for words like borrowed Proto-Germanic *kuningaz and *wīsaz, which became king and wise in English, but kuningas and viisas in modern Finnish. So you can have both phonemic writing as well as etymological transparency if your phonology doesn't change much.
That is indeed a problem with English, but even then it is possible to come up with a morpho-somewhat-phonemic spelling that would be far more consistent than modern English - because the bar set by the standard orthography is really that low.
And OTOH even modern English spelling often doesn't distinguish differences that are there in most dialects (e.g. "bear" vs "near"), so this isn't even a new problem. Realistically I suspect there's some "minimal reasonable set" of phonemes that need to be distinguished to reflect the most prominently distinct pairs in all major dialects, even if some subtle dialectal distinctions might not be reflected in spelling.