"Charlie X" is the start of a long tradition, in shooting but not broadcast order preceded by "Where No Man Has Gone Before," that saw the franchise repeatedly explore the concept of a character gaining extraordinary abilities (other examples include Riker in "Hide and Q" and Barclay in "The Nth Degree," both The Next Generation, as well as Dukat in "What You Leave Behind" from Deep Space Nine as well as Sisko throughout the series, plus Wesley throughout Next Generation but notably in "Journey's End").
The title character is also the first of many in the franchise to be a lone survivor who must try and reintegrate with his regular life (so many examples it suffices to say Worf is the most famous example aside from numerous guest characters).
Charlie is reminiscent of the boy Bill Mumy played in "It's a Good Life," one of the signature Twilight Zone episodes, originally broadcast in 1961. Star Trek might have ended up being viewed as a more bug-eyed version of Twilight Zone had more comparable episodes been produced, and perhaps at the time such associations were part of the reason it had such a weak lifeline.
In the end, the biggest mark of distinction for "Charlie X" might once again point toward Wesley. Both are troubled boy geniuses who struggle with fitting in.
Absent from the episode are the characters of Scotty and Sulu. Uhura is here. She even sings. Charlie obsesses over Yeoman Rand, the original Star Trek sexpot.
franchise * series * essential * character
Grace Lee Whitney
Memory Alpha summary