"Star Trek Beyond" co-writer Simon Pegg (Scotty) explained the reasoning to Star Trek Podcast (via JoBlo):
Pegg said they did have a brief explanation of her absence in the film -- a draft of the script saying Carol had gone off to start work on Project Genesis -- but it didn't make the final cut of the film.
"With this it felt like we would under-serve her if we included her, she might end up feeling like she hadn't been given the amount of screen-time she deserves, so rather than bring her in and just have her be a supporting role, like, have her not be in this one, and when the time comes [bring her back], the worst thing to do would be to have her in the film and have that character be killed, and that felt like a cynical thing to do. We thought rather than have Carol Marcus not be used to a reasonable capacity, let's just not include her, have her be alive, in canon, and ready to come back at any time."
"Star Trek 4" is already in the works, and it's possible Dr. Marcus can return for that. Do you hope she does?
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