Earlier quoted context omitted.
When you notice these flaws you are seeing it in very very short term. What we are today is what eventually worked for a million years. The design you see today is the way it is because it had to be robust enough (including those problems) to survive to this day. The examples you quote do look like a problem today, but I think they must have worked to some benefit to bring us here.
Yes, you’re describing evolution.
If anything, your optimal design is just another mutation that may or may not survive time.