I totally agree, it is a well-balanced story. But I guess it was perceived as too cerebral by the powers that were because of Pike's doubts, Number One and the sexual stuff about Vina wanting to be young again and so on (or rather the way this was handled, with cold distance). I think it is more a matter of overall atmosphere and The Cage was certainly THE Trek story which was most inspired by Forbidden Planet. I'd even claim that it tries to replicate its atmosphere.
Talking about Forbidden Planet, it is as if somebody perceives Forbidden Planet to be too brainy because of the monster from the id or rather their ids. A tiny touch of vulgar psychoanalysis does not really make the story utterly brilliant or too difficult for anybody to understand but I can see why studio executives might think so.