Deadline and confirmed by other media sites that Paramount has fired Roberto Orci as director of Star Trek 3. According to the site, "Rampant rumors are swirling and I’ve confirmed there is fire behind the smoke that he won’t be directing. I even hear that Edgar Wright and others are on a short list to take the job. Orci stays on the project as producer, I’ve heard." The exact reasons have yet to be revealed (and unlikely will be). No replacement director has been announced but its probably early enough in the pre-production process that as long as Paramount does not drag their feet on finding a replacement they should still be able to get a 2016 release date.
It reads that he is essentially going to be completely removed from any involvement in the film a producer credit is more of a contractual thing than anything. Most films have at most one or two true producers that is on set and making decisions day to day with the rest of the list just names that were in some tangential way involved in getting the film financed or sequel carry over. In a weird way think of an executive producer as CEO of the movie, most of the other producers as vice presidents with one of the lot chosen as the project manager. Like at big companies, only the project manager is involved in the day to day decisions because their key job is to keep things on budget and on time. The support of the other VPs (other producers) and CEO (exec. producer) is necessary but their actual influence on what becomes the final product is minimal. So in this case Orci will likely get a producer credit but his ability to influence the movie that becomes Star Trek 3 is now at an end as probably so his involvement with the franchise as a whole (including the IDW comics). Since his work on the films has been a collaborative effort requiring him to mostly bend his desires to meet those of Abrams and others higher up the food chain, we really have no idea if this is a massive missed opportunity with a true Trekkie at the helm or a dodged bullet. Sadly we probably will never know for sure.