Gene Roddenberry had some great ideas. He also had a lot of really damned terrible ideas, and wasn't very good at handling a show with a hands-on approach. I respect him for creating the franchise, but in my opinion, Star Trek was only at its best when he didn't have his hands on it. Rick Berman, who catches a LOT of flak (some justified, some not) honestly did a pretty okay job running things and was a fair sight better than Roddenberry; I think a lot of problems with Berman came down to being too used to ST after a while.
The tl;dr version is that Roddenberry was a visionary in a way, but like every visionary for an entertainment genre, he was also friggin' nuts.