ST'09 was filmed during the writer's strike, so they weren't allowed to make writing changes on the fly for that one.
Not during most of shooting, but definitely toward the end and in editing and post-production. You'd be surprised how much a film's content can be changed after filming by redubbing and selectively editing the dialogue. I recall reading an article about how they were actually able to use CGI to alter Leonard Nimoy's mouth movements to fit redubbed dialogue. My understanding is that the entire Spock Prime mind-meld sequence, which contains the most ludicrous science in the movie (the whole ridiculous portrayal of the supernova and how it's "stopped"), was constructed quite late in post-production and was substantially altered from what was originally planned.
Now, if you think the films that Orci and Kurtzman had a hand in producing were unsatisfying, that's your prerogative. I'm just trying to clarify the process. As a general rule, unless the credited writers of a film are also producing or directing, you cannot safely assume that the finished film reflects what those writers actually wrote in their drafts of the script, or what they would have written if they'd been controlling the process rather than following the director's orders. You can't even safely assume that the credited writers are responsible for a single word of dialogue you hear in the film. That's why so many Hollywood screenwriters have their names on films that run the gamut from brilliant to awful.