What makes you think that Uhura was not a linguist in the prime timeline?
Because she was a communications officer in the prime timeline? She is a communications officer in the alternate timeline, too.
According to Nichelle Nichols and her book Beyond Uhura, that's exactly what Uhura was supposed to be, according to the backstory that she and Roddenberry originally created for her...
True, they didn't show it on screen, but they never said she wasn't a linguist, either, did they? The only thing that contradicts it is the stupid scene that they included for laughs in TUC.
For starters, Nichols' opinion of her character has little bearing on this point.
There is nothing in TOS or the films to suggest Uhura is anything other than a talent communication system technologist.
1) Uhura is never said to be a linguist.
2) Uhura never speaks anything other than English or her native Swahili.
3) Uhura needs a universal translator or books in order to badly speak Klingon.
4) Spock states that Uhura is the most qualified to repair her communications equipment -- link: http://tos.trekcore.com/gallery/albums/2x02/WhoMournsForAdonais0273.jpg
5) Uhura initially wore the gold command uniform in "The Corbomite Maneuver" and "Mudd's Women" but wore the red uniform of engineering and support services for the rest of the series. Linguistics is part of the field of anthropology, and the Enterprise's anthropology officer, Carolyn Palamas, wore the blue sciences uniform.
6) M5 selected her as a critical officer for the war games.
7) Uhura was overseeing the communication systems during the TMP-era refit and the TFF-era system repairs.
8) She was assigned to a transporter technician in TSFS.
So there is no evidence (other than Nichols' insistence) than Uhura was a linguist, and all evidence points to a skilled system technician.
The question is: What's wrong with that? Why is it better or more acceptable for her to be a linguist than a communication system technologist? Both should be considered respectable careers.