A certain guy who was a supervisor at the train station in the U.S. while talking to two federal agents, said:

And let me tell you, nobody from the federal government tells us s.h.i.t. about anything. Hell, a lot of them question why the country needs trains at all. What with the highways suffocated and the skies filled to overflowing and every civilized country in the world building trains and rails at record paces, you'd think they could figure it out for themselves.

I'm not sure I understand these two bolded phrases.

Maybe the first one means: Look every civilized country builds .... ???

As for the last one I think it refers to people from the federal government, but I'm not quite sure what that guy wanted to say?
" What with the highways ------" The phrase "what with starts the list of reasons for the need for the trains"

"you'd think they could figure it out for themselves." They = the government in this case. He feels they should be able to deduce from the list of problems that the country needs trains.
1) Instead of providing a straightforward answer to the question "why the country needs trains" (for example the author could have said "Because the highways are suffocated and the skies are filled to overflowing" ) the author chose to answer that with a declarative sentence that resembles a question (What with....)

2) It simply means that they (the government people) would realize that the country needs new trains and rails without having anybody else tell them that.
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What with the highways suffocated = Since the highways are suffocated
you'd think they could figure it out for themselves. = The gov't people should be able to understand the situation just by observing the world conditions (crowded highways, railway construction, etc.)
 Ivanhr's reply was promoted to an answer.
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Thanks for these informative answers!