I'm sad at how few characters from literature are on the list. I've never seen a movie or TV show that could expand on a character the same way a savvy and intelligent author could.
Isaac Dan der Grimnebulin of China Miéville's Perdido Street Station is the quintessential archetype of the scientist in science fiction literature. He's driven, brilliant, and perhaps too curious about the workings of the universe for his own good. It's his lack of discipline and his limitless imagination without fear of consequence that lands him in trouble, but his brave, inquisitive and thoughtful nature could be his salvation. You'll have to turn off the TV and read Perdido Street Station.
Charles Lindbergh in Philip Roth's The Plot Against America is one of the most incredible and terrifying recreations of a historical figure in the genre of alternative history. The Plot Against America, some may know, is a novel speculation about an alternative history in which aviation legend and American national hero Charles Lindbergh defeats FDR in 1940 and, because of his isolationist ideologies, signs a peace pact with Japan and Germany. While the story is about a particular family living in this alternate reality, the most striking character in the novel by far has to be a man now regarded simply as a brave pioneer in the earlier days of manned flight who was actually—and this is supported by historical fact—a strict non-interventionist and anti-war advocate during World War 2, Charles Lindbergh. While not a protagonist, his character is truly fascinating.
Finally, there's Christopher John Francis Boone, protagonist of Mark Haddon's The Curious Incident of the Dog in the Night-Time. Christopher is a fifteen year old (likely) autistic boy who lives with his father, his mother having recently died, who discovers a dead dog which sets off a chain of events that change his life. The character of Christopher John Francis Boone hearkens back to Salinger's Holden Caulfield as a highly intelligent and troubled youth expertly written, someone who, despite having troubling characteristics, is incredibly relatable. Throughout the story, Christopher grows naturally as a character and going along for the ride is very enjoyable.
And of course there's Bill Adama of Battlestar Galactica and Jean-Luc Picard of Star Trek: The Next Generation.
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