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Confused clearances are a root cause behind thousands of pilot-controller misunderstandings, as well as many violations and accidents. That's a sad fact, as the whole point of the clearance is that controller and pilot share a common expectation as to where the aircraft will go and what it will do when it gets there.
The problem isn't so much that there are so many different means to reach the single goal of landing at your destination--multiple route options, multiple altitude options--but that, practically speaking, you can't always work out the ramifications of a clearance right away. This means you're often signing the contract before you get to read the fine print.
