Even on the original Star Trek, Gene was clashing with the writers. Gene Coon really was able to help shape the series and made a lot of it work. Same with Piller on TNG. He was in the middle of what the writers wanted to do, and what gene wanted, and then deciding what was best for the show. Also not being allowed to mention the old show was just a stupid decision. It would have helped connect the two shows.
I just find it interesting that Star Wars is now at where Trek was in the 87, and in 09 Star Wars fans want to deny it, but that franchise now needs to get beyond the "Lucas box" to survive.