It causes more problems in languages that have a writing system convention that is more opaque, such as English, Chinese or French, and less problems with languages with more transparent writing systems, such as Turkish or Finnish. A transparent system means that spelling is more predictable and there is often a one grapheme = phoneme relationship.
There's a great deal of conservatism in spelling, and perhaps that's good because it means that it's easier to understand old texts and you don't have to update everyone on new conventions every year. It makes national standardization easier too, which can be an important factor in equals rights of all citizens. But sometimes, you know.. it just gets to me on a personal level. Especially <i> and <e> in English, mein Gott.
I guess we can also imagine such a thing as "Phonetic Eyes", that would mean trying to depict sound as it was just in that instant by that speaker etc and not just the most common way of pronouncing that word.
Any one out there with "Phonetic Eyes Problems"? I'd love to hear 'em :)!