I'm continually baffled by the fixation on the director as the salvation or damnation of the films. He doesn't write them.

Star Trek was penned by Orci and Kurtzman and overseen by at least five exec producers all of whom would have had a hand in a) the sacrilegious violation of canon when turning the Star Trek universe into one which dealt with a pin-headed plot of good versus evil; or b) the refreshing reboot of an ageing and overly-optimistic world mired in a 60's mentality. Pick one.

Between them those two were also responsible for The Island, Transformers and Cowboys And Aliens, those paragons of thoughtful, profoundly philosophical SF. Orci exec produced The Proposal, for Zeus' sake, a film in which one of the highest ranked scenes of comedy features a lapdog being savaged by a hawk.

Abrams himself could have directed Phantom Menace and made it edgier, more gripping and a more memorable film even given the breath-taking failures in the script because he's a good director. He would have made some executive calls in the plotting, probably, and they would have improved the final cut. However fundamental hinges to storyworld logic are choices made far earlier.