As many authors have pointed out, English is a historically phonetic language but as sounds change over the centuries spelling and pronunciation drift apart. Hence today "love" and "cove" no longer have the same vowel sound, but back in the late 1500s they did. It's not surprising that our "ough" and "augh" compounds likewise show a great deal of phonetic variance. While this confusion can theoretically be mitigated by adopting a purely phonetic spelling, the problem then becomes: whose phonemes do we choose? If we ask someone from Texas for the "correct" pronunciation of "pen" we will get "pin." British speakers can be assigned a class based on their pronunciation of garage. And so on. Thus we're left with a problem however we choose to proceed.