Science fiction has been described as the genre that, by addressing the future,
that it concerns ideas of large scope rather than the ephemeral thoughts and emotions of individuals.
A. that it concerns ideas of large scope rather than the ephemeral thoughts -> 1st "that" is used in non-underlined part, which is acting as conjunction, we don't need another "that" followed by "it". Incorrect.
B. that concerns ideas of large scope instead of the ephemeral thoughts -> "instead of " is used for "in place of", here we have contrast usage. Incorrect.
C. concerns ideas of large scope rather than the ephemeral thoughts -> It is better. Let's keep it.
D. so concerns ideas of large scope instead of the ephemeral thinking -> Same as B.
E. it concerns ideas of large scope but not the ephemeral thoughts -> "but not" is not giving contrasting meaning.
So, I think C.