1. Nobody said they were perfect. Nothing is perfect. Only Socialists believe in perfection.
2. If you take an imperfect system and further devalue it by playing 8 vs 4 and 1 vs 5 then you are saying basically "who cares about the ranking". Making the rankings even more imperfect, in a sense, needlessly...
3. Nadal and Djokovic should not have met in the QFs, even with his 5th ranking. In the 90s it was 1/2 vs 7/8, meaning that 1 vs 5 was not allowed, not possible...
If they were to draw by ranking it wouldn't be 8vs4, 1vs5 etc. It would be 1vs8, 2vs7, 3vs6, 4vs5. The 5th ranked player is protected relative to the 8th ranked, and #1 is protected relative to #4.