Deep Space 9 would be really different. There would be no Dominion War for certain. Admiral Leyton would never attempt a coup or if he did he would turn out to be an alien, perhaps a Founder. The Klingons might not have returned to their old ways. Star Trek: First Contact might have been different, though there are some parts of it I could see Roddenberry liking. Voyager and Enterprise would be butterflied away. There might have been a Captain Sulu series. Then again, I have no clue if Roddenberry would have supported one or not. If Earth: Final Conflict and Andromeda were even made, they would have been different, potentially even existing within the same universe as each other and possibly even that of the Star Trek series.