This is a problem that other languages have already dealt with. Spelling doesn't have to represent the exact pronunciation of every word; it can represent phonemes, leaving some variation in pronunciation to dialect.

For example Vietnamese has considerable regional variation, some of which is reflected in the spelling system. The letter d represents /z/ in standard Northern Vietnamese but /j/ in standard Southern Vietnamese.

English already does something similar, as you've pointed out. In dialects that distinguish wh from w, the former can represent /hw/, whereas in most of England the distinction has disappeared and both are pronounced /w/. We don't need to respell whale because it already accommodates either pronunciation (although let's please get rid of "magic e" and spell it `wheil` to at least match the vowel).

Any linguist knows that a perfectly phonetic spelling system is not desirable. As well as what I've already discussed, pronunciation changes over time too. But I don't think that rules out spelling reform because currently English has many ways of spelling the same phoneme.

I just want "a" to make the same sound it makes in literally every other spelling system, including Cyrillic and Greek, not "ey" or "eh". Seriously, that's one of the most stable phonemes, how did it turn into "ey" in English?