So the question becomes: why is Into Darkness rated higher than Beyond? Again, this perplexes me as well.
Quick answer: The Sins of the Father
Why that's my answer
The brands fragile and foothold in the public sphere created a narrative momentum to the collective consensus that, I believe, couldn't be accurately captured in a snapshot.
By the time Beyond was a thing, the overall enthusiasm for the brand was that much lower.
Why ITD got good reviews but ended up doing that?
First of all I would say that IDT has the dubious distinction of being an... ok... movie but a terrible sequel and that what ITD and 09 both needed to do as products beyond just being 'good' was different.
The thing is 09 did NOT prove that StarTrek was viable again as a continuing film series. It the first half of a two part question of viability that was not a conscious thought to anyone but the actual StarTrek
fans.
09 demonstrated that you could update Trek and make the base world and characters 'work' even if it meant hanging them on a lattice of being a typical summer blockbuster (let's be honest, you could have redressed 09 as any fictional world Andy the film would have worked). Something both necessary and thought impossible.
It wasn't fully formed in that it didn't go full Trek in seeking out new worlds and new civilizations, but that wasn't its job. It was very much setup for the promise of the premise.
There's something about being a child of two worlds here that I can't quite pull from the either of my mind, but act two of doing the impossible was very much to show that you could have the full soul of Trek in the body of this template and make both sing in unison.
The problem then with Darkness emulating 09 so closely while being at best Inferior? In the moment that was certainly enough to get decent reviews and user scores but it utterly failed as a sequel and in sustaining interest in the brand.
Partially because the fridge Logic was just that bad and partially because it declared to audiences casual and hardcore alike that the brand had nowhere to grow. So the more casual audience members and mainstream critics who probably reviewed it as a summer blockbuster had no reason to tune in for the next one or passionately advocate in its defense. They got the formula and truth be told it wasn't all that different from what anyone else was doing, except this one makes StarTrek references.
So it's easy to then understand why the people who were passionate about it tended to fall into the camps of being passionately underwhelmed and offended. Those are the people who shaped the discourse and public consciousness of the Kelvin timeline films in the years leading up to Beyond, and I don't even think that they were fringe for having done so.