Many fans cite what Gene Roddenberry would want from Star Trek but he hated most of the things fans loved

Without Gene Roddenberry, we wouldn't be here writing about Star Trek. There is not a single person in this world who can debate that fact. Yet, with Roddenberry, the franchise may never have survived the 1980s. People often forget that Roddenberry was only really around for the original series run in the 1960s and then for Star Trek The Motion Picture.

The second film in the franchise, all the way to the start of the Next Generation, was not produced by Roddenberry. He was removed from his position of power by Paramount after the failure of the first Star Trek film and wouldn't be brought back until production of the Next Generation had begun. He was kept on the payroll during those in-between years, but he had no power or say over things anymore.

So much so that he tried to ruin Star Trek: The Wrath of Khan out of spite, by telling fans the big twist involving the death of Spock. So it's not surprising he wasn't going to be easy to work with come the birth of the Next Generation. Various people have talked about the struggle that the crew at the time had working with Roddenberry, with former Star Trek lead William Shatner telling The Hollywood Reporter;

"The fights that went on, to my understanding, were big because the writers had their difficulties. ‘We need some more material.’ ‘We need to get out of here. It’s claustrophobic.’…I haven’t watched the other Star Treks very much, but what I’ve seen with glimpses of the Next Generation is yes, the difficulty in the beginning, between management, was all about Gene’s rules and obeying or not obeying those rules.
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There were conflicts all the time, usually about the best aspects of the show. Roddenberry didn't want to focus on Klingons, Vulcans, and Romulans anymore. Instead, he wanted a wider focus on new aliens. He wanted new technology and less inter-office intermingling. He also didn't enjoy the films coming out after the start of the new series.

Claims made by Shatner and Leonard Nimoy say something different. In their books, they reveal he disliked a good deal of Star Trek VI: The Undiscovered Country and wanted nearly 20% of the film changed. To no avail, however. He, thought, largely that the Federation wouldn't hold biases against the Klingons. Despite the Klingons being, well, Klingons.

Roddenberry's involvement in Star Trek should never be dismissed, but it's worth saying the franchise has become bigger than just one man. It's no longer just Roddenberry's baby, but the idea of dozens, if not hundreds of people. When some of the best work came out despite what Roddenberry wanted, it's fair to cite what he would or wouldn't like.

Considering he liked very little, it seemed.