As a lifelong Star Trek die hard, I very visibly and physically cringed when Christian defended any of this as a remotely cerebral or even classical Star Trek. I enjoyed this movie as a silly action scifi movie, but this is Trek purely in name. To be fair, none of the Star Trek movies are terribly true to the original notions of the Trek series, including the movies where Gene was involved in the production, but these are in a league of their own. Apologies for the length of this comment!
At it's core, Star Trek is about man's struggle with our darker impulses, and understanding our role in a barely understood universe. A key theme is accepting that our understanding of universe, no matter how advanced our science or technology may seem, is still in its infancy. The JJ Abrams line of Trek films is that it really only pays lip service to these ideals.
The most obvious example I can give is the perpetually unbelievable, unexplained escalation of technology and threat. All three of the Abrams' Trek movies revolve around these unexplained technological threats that are an immense leap forward in technology, but I'll focus on Beyond.
Comparing Beyond to Undiscovered Country; the central threat to both movies is a rogue element with some form of advanced weapon or technology. In Undiscovered Country the threat to peace is a Klingon bird-of-prey that can fire while cloaked. In the Trek setting this is a superweapon. Cloaking technology is clearly understood, its strengths and weaknesses are defind. While cloaked, a ship cannot travel at warp speed, fire weapons, or raise shields; they are undetectable but exposed.
The ability to fire while cloaked isn't a doomsday scenario; it's not going to wipe out planets or space stations. While a devastating technology, its strengths and weaknesses are clearly explained and demonstrated in the film. This technology doesn't defy any of the known and understood constants of the Trek universe without explanatio. Perhaps most importantly of all, this technology seems to be designed to compliment the core conflict of the story; a rogue Klingon using subterfuge in an effort to prevent peace, avoid blame, and frame the Federation.
The threat in Beyond is a swarm of navigable, nearly indestructible drones, capable of shredding through a star ship, and possibly a space station. This technology is largely unexplained, and violates not just the constants of the Trek universe without justification, but even our modern understanding of science.
For instance, we can clearly see those drones shearing cleanly through the Enterprise's hull. The drones do not appear to suffer any damage, or even lose momentum while seemingly effortlessly cleaving through the hull. From this, we can only infer that these drones are constructed from sort of undiscovered super-dense material, but this is never questioned or explained. Why are none of the science or engineering officers puzzled at this new marvel of technology? No one stops to consider what this technology, produced on a mass scale, would do in the larger universe.
The writers don't want you to think about it, because it's a big dumb action movie, and I enjoyed it as a big dumb action movie, but it's not Star Trek. I believe that is what Tom means when he said it's not cerebral.