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RE: Klingons
In this new timeline, if memory serves, didn't "Star Trek" talk about the Klingon Empire getting decimated by Nero and Uhura hearing about it. Are they using that to avoid Klingon movies?
Also, in The Undiscovered Country it talks about Kirk hating the Kilngons for killing his son, which is weird to me since I didn't know he ever had a wife/kid. But, now he obviously wouldn't have that drive since he has no wife/son.
I don't remember. All I remember is that Admiral Marcus believed that war was all but inevitable with the Klingon Empire. I think they've largely been avoiding it because that's a lot of what TOS era dealt with anyways was the discord between the Klingons and Federation, but hell they brought in Khan in Into Darkness so...
As to your second bit, Carol Marcus was the mother of Kirk's son David Marcus in the prime timeline, which was revealed in The Wrath of Khan. David was subsequently killed by the Klingons on the Genesis planet in The Search for Spock. Carol Marcus was in Into Darkness, but no where to be seen in Beyond and I don't remember any mention of her either. So she might have left the Enterprise in the intervening time while they ship started its journey and Beyond,
which is apparently the reasoning that Simon Pegg decided not to include the character in the film. Now Pegg's idea of her starting to research on the Genesis Project to explain her absence I'm not too crazy about, but I could deal with her leaving the crew at some point for other reasons like a different project that isn't a complete rip-off of something we have already seen in the prime universe.
Depending on where they go for the fourth film and amount of time that passes, they're obviously going to have to explain Chekov leaving the Enterprise and replace him with someone. They could explain it as him having been promoted and taking an executive officer on another ship that's not named Reliant.