You are right in saying that the different forms of spelling of plurals with ‘y’ is due to the fact that this letter can be used as a vowel or a consonant.
In the word fly, for example,’y’ is used as a vowel and so changes to ‘i’ in plurals. In the word ‘play’, ‘y’ is considered a consonant and so doesn’t change. A clue to help you here is that you have a vowel (‘a’) before ‘y’.
Students can usually understand this and exposure to many examples over time will help them tune into the rule.
You ask why we don’t simply standardise the formation of plurals. I suppose the answer is that English is a living language, rules are not imposed, they emerge through usage. However, there’s no reason why we wouldn’t move in that direction over time. This is a very long process though.