"Gene's Vision" has been an effective marketing strategy for the franchise since the seventies, but as many others have posted, it doesn't have much concrete meaning because it (a) exaggerates Roddenberry's status as a "visionary," (b) gives him credit for the creations of others, and (c) has been constantly revised to sell whatever the latest product happens to be.
No doubt the phrase has and (to an extent) will continue to be effective as a marketing tool, but I also find—on message boards such as this—that its utterance may signal the onset of a load of sanctimonious claptrap in the form of mantras like:
"_____ is a slap to the face of _____" or
"_____ would have _____ spinning in his grave" or
"no True Fan of Trek™ would ever accept ______."
"Gene Roddenberry's Vision™" is too often invoked as if it conveyed instant legitimacy upon the maker of any solemn or zealous pronouncements which follow, when all they usually are is just so much hot air standing in for "It's not what I would have preferred to see."