I'm still hoping they pull a Doctor Who:
-The new series was a completely new type of television and storytelling
-It's main focus was to introduce the show to people that have never seen it before, and only having small "nods" to the past for the old fans
-It still was "officially" set in the same continuity as the rest of the franchise
-There were even small cameos (Sarah Jane, K9) and returning monsters (Daleks, Cybermen) from the old series
-They completely ignored the "reboot"-movie that was made inbetween (the one with McGann, where the doctor was half-human). At least continuity wise. They still aknowledged parts of it in retrospect. Ignoring the changes and the plot of that movie, but accepting McGann as one of the doctors, and even giving him a small cameo in an Internet special later on.
How would that work in Star Trek? Be set in the prime universe. Ignore what happened in the JJ-reboot movies. But accept Pine, Quinto and the rest of the actors as part of the franchise. Ignore the plot and timeline split, ignore the destruction of Vulcan and/or Romulus, ignore the worst parts of JJ-Treknology (like transwarp beaming, curing death, way-too big starships, most of which Beyond already ignores). But pretend Chris Pine and Shatner were the same person, that lived in the same universe with Picard and Sisko. If that should ever be mentioned. Which it should only in small doses. Very small ones.
I confess I do see parallels between Doctor Who and Star Trek's situations - both taken off the air after a long continuous run; 10+ year TV gap with books, and a couple of one off screen returns (Trek got 3 movies, Doctor Who got a 1996 TV movie and 2 charity specials [Dimensions in Time and The Curse of Fatal Death]); both being revitalised by known fans with a respectable TV portfolio