Regarding the future of Star Trek, Gene Roddenberry had this to say in an interview:

Several years later, at a Star Trek convention in Los Angeles, about a year before his death, Gene Roddenberry spoke to the gathered fans about the future of Star Trek. He had seen his creation span generations of viewers, he had heard the fans of both The Original Series and the new debate the pros and cons of both, and though there had been no formal talks of a third series at this time, he spoke of how he perceives Star Trek's future, after he was gone.

With a charm and sincerity that clearly came from a person who was used to studying human behavior from the perspective of one who looked into the future, Roddenberry said that he expected -- indeed, he hoped -- that in the years to come, new generations of fans would look at the new forms of Star Trek beeing produced and say, "This is real Star Trek. Those other people back there at the beginning, they didn't do it half as well."   

(from The Making of Star Trek: Deep Space Nine, p. 49)

After Roddenberry death there was a new team lead by Rick Berman and Brendan Bragan. And perhaps it is only a coincidence?! But the new series changed the Star Trek universe little by little. And at least, everything from Roddenberrys StarTrek (see the Original Timeline) is now changed.

When the show was over, I called Dorothy at home. "What happened?" I asked her. "I thought you said Gene loved
my script!"

"He did," she said.

"But he changed it. He changed every word."

"That doesn't mean he didn't love it," said Dorothy. "But Star Trek is his universe, and he wants it exactly his way."

Larry Brody 10.6.1996, http://www.tvwriter.com/startrek4.html

Roddenberry had a clear idea what is StarTrek and what is not. He did not invent the full universe.

Gene rewrote virtually every Star Trek script for the first two seasons, often working around the clock, days at a time, to produce scripts that conformed to his view of what Star Trek was and could be. It was not unusual for Gene to be walking out of the studio in the morning as the actors were arriving.

As Gene used to say, "It isn’t Star Trek until I say it’s Star Trek." This ability to synthesize and improve input from others, adding his own special insights and touches, is best illustrated in the famous opening that set the tone for the series.

At first i wondered about the different Trek universes. Now i am for sure, that someone wants to make Star Trek to his Star Trek. It is not longer Roddenberry and his team who made the well known universe with Klingons, Romulans and Vulcans. Their original work has been rewritten and is now something else. Here I named it Paramount-Trek.