The Justman sounds plausable, they might have also have had an issue with the sexual themes of "The Cage".
Anyway, pointless to debate such background issues, you just gotta watch the two pilots to realize that the first one is not merely more cerebral and sci-fi-ish than the second one but also more memorable and popular.
Doesn't mean these qualities are always good, it is e.g. unbearable to watch a movie like TMP.
About classical sci-fi movies, if you ignore the B movies (on the big screen WNMHGB would have been a B movie) they are overall far better than contemporary sci-fi movies. It is not incidentally called the golden age of science fiction.
I've seen both many times and I can't see why "The Cage" is more cerebral, other than being told that it is so many times that we've come to believe it. Same for the "sci-fi-ish". Care to explain? Tell us what's more cerebral and sci-fi-ish about "The Cage"? At best I'd say its more cinematic.
Oh, so we have to eliminate the B-movies to find what's "typical".
You must have a different definition of "typical".