Orci and Kurtzman were reportedly actual Trek fans. Therefore more love and familiarity = a better movie. Oh and J.J Abrams actually knows how to work with characters.
In contrast with transformers however, orci and kurtzman involvement with the franchise was basically 'yeh we watched the cartoons as a kid, wouldn't a movie be cool?'.
Basically I feel that not enough love, respect and understanding went into the transformers film (on a leadership level).