Best case for Star Trek Beyond:
-Paramount pulls Star Trek back from it's tentpole position, and back to it's original niché, with future products being aimed at a smaller, but more reliable audience (resulting in smaller budgets for future movies, but less meddling from the producers)
-The JJverse is put to a rest, any new Star Trek product tries to 'reconcile' with it's original audience
I disagree that this would be a "best case". Star Trek is not designed to be used as fodder for an art film or an indie-style Oscar bait film. It is too silly for that, uses too many gee-whiz tricks, and is too firmly linked to popcorn style flicks to get away with becoming a niche. If Star Trek stops being a viable tent-pole summer flick franchise - it dies.
The same thing happens if anyone attempts to resurrect the "Prime" timeline.
Nah. Star Trek will never, ever go anywhere even NEAR an Oscar. But the summer tentpole spot is also wrong. JJs 'Star Trek' was the first Star Trek movie that tried to be a summer blockbuster. As a result it was less "Star Trek: The movie" and more "Star Trek: the ride". Very entertaining and fun to watch, but essentially a 'best-of' of everything Star Trek, without a coherent plot or even a point to make. They never tried to do something new, just do the old stuff in a bigger way (Time Travel! Kubayashi Maru! Transporter Accidents! Red Shirts dying spectacular! Planets being destroyed! Mind Bugs! San Francisco LAZERED! Ship vs. even more giant ship! Black holes! Warp core breach!). That's the reason for the nose-dive that is 'Into Darkness': they already rehashed everything big and important in the first movie, there was nothing left to top that anymore. You can't get bigger than destroying Vulcan and nearly Earth.
I would love for the Star Trek movies to take a step back, to where they originally where, in the prize range of Star Trek: The Motion Picture to Nemesis, with appropriate budget and box office expectations. Aimed at the more traditional Star Trek audience (Fast and Furions never aimed to be big. They just stayed true to their original brand, and more people hopped on. Star Trek tried forcefully to be big). Once you go over 100 mio.$ budget, you have to please everybody, and any Producer with a dumb idea is adding his own suggestions, and the movie is more driven by marketing studies and release dates than by someone wanting to tell a coherent science-fiction story.
Never gonna' happen though. The new movies are not that big of a success, but make enough money to get the Spiderman-Treatment and will be either be continued or Rebooted, whatever to churn out one movie after another, trying to keep the brand at the market.
That's why I would like Star Trek back on tv, in the best case in the DC-version, with big blockbusters (Man of Steel, Batman v. Superman) for general audiences and a seperated continuity on tv ('Arrow' and 'The Flash'), preferable the old 'prime univers', that don't intermix, so that the tv series could go on, while the movie series is able to do whatever it wants without being bound by continuity.