I think the issue with Orci's script was just Shatner and the use of time travel. Those were elements the studio didn't like, not the stuff from that quote.
Regardless what Pegg and Lin claim, there were similarities between that story and beyond that probably was the cheaper version of what trek 3 originally was supposed to be.
I'm not saying Pegg and Jung plagiarized anything or they didn't have ideas. I can believe them that they didn't read Orci's script, but the producers did and told them to put X, y and Z in the movie, IMO. Even gay Sulu was something JJ himself had wanted to imply back in stid, yet Pegg kind of tried to get kudos for being innovative as if he was the first to even think about having non-straight characters when JJ had previoustly stated they had an idea for one and Orci confirmed it was Sulu in his movie too.
When the first trailer came out, Orci&co still got a credit, much to Lin's annoyance. Why?
Once you write a script for a studio, they own it and can use it.
Writers, for better or worse, get all the blame or praise but you gotta ask yourself how much of a script really is the story they want to tell and how much it's the studio and producers demanding them to write a script around their ideas.
I think jj&co probably had more real creative freedom only when they made the first movie. From stid onwards, including lin&Co, I have my doubts they were truly free to tell all the stories they wanted.
Based on those ST3 tweets orci did couple years back - think the device that krall was after in Beyond (that did what again? idk) was the time travel device in Orci's ST3 (similar to the ones in Prince of Persia and Tomb Raider1?) Krall and Co will have been the 'Annunaki' (with same makeups as Beyond? and the swarm too?) who are like ancient aliens seeking to restore the timeline? (thus wiping out kelvinverse) and maybe it'd have played out something like The Chase where everyones after the device (probably Klingons & Romulans too).. Kirk & Spock get roped into it all and are tempted when they realise they can change the past (Spocks mother/Vulcan, Kirks father)- but ultimately decide against it (so it becomes like a battle to save the Alt timeline? - the opposite of stuff like YesterdaysEnt). Shatner Kirk 'Prime' must've been brought back by the device somehow (by Nimoy Spock to help K&S?) and maybe it would've ended with Shat Kirk having to sacrifice himself to protect the timelines? (but in a more meaningful epic way than Generations)
and then of course elements of that mustve been rewritten into the ST4 with Hemsworth instead of Shatner
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