1. The designer does not have to be "omniscient" only intelligent. Some people believe in it's omniscience but I don't think it's a requirement.
2. How do you know that our trachea is not an optimal design when you take into account all the tradeoffs?
3. You're surrounded by items created by intelligent design (us) and all of them have flaws, reused parts and tend to break. Obviously you wouldn't argue based on this that they weren't designed by intelligent beings.