Re: How come & why
The difference between "how come" and "why" I think is that "how come" seems more conversational than "why." I also agree that "how come" often implies that there is some doubt. Like when you ask a question beginning with "how come..." the implied rest of the sentence is "instead of..."
But they're not interchangeable grammatically. In fact, I can't think of a sentence beginning with "why" that you could replace with "how come" without switching other words around.
"How come you didn't see the movie with them?"
"Why didn't you see the movie with them?"
or
"Why did you go to Peru?"
"How come you went to Peru?"
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