It's rather strange to say that Roddenberry had more influence over Deep Space Nine, Voyager, and Enterprise than StarTrek2009. He wasn't alive for any of those works, but his *influence* was on all of them. In fact, one could argue that he had more influence over StarTrek2009 as it was based upon characters he directly controlled/created.
Edit:
I suppose we could call them the Prime Universe and the SubUniverse.
Edit:
I suppose we could call them the Prime Universe and the SubUniverse.