The "sins" of Into Darkness got immediately/drastically overinflated by Star Trek fandom.
Into Darkness is an all round terrible movie that really should not be high on anyone's 'good movie' list. Hell, the first shot is "planet Nibiru" which is a direct reference to Von Daniken's crap and has since been co-opted by conspiracy culture, meaning that the first shot immediately ties it to a whole host of nutcase shit, including the anti-Semitic variety. Yeah, this is a great way to start something.
(I know this because of reasons)
And then you see the rest of it, and completely forget like, two hours later. Not kidding either, I rewatched it last month and I've frankly already forgotten it. There's nothing there of worth, unless you think random nudity or ass-shot while approaching Klingons are somehow good things. (seriously, wtf is the context of that shot? Are we supposed to fear this engagement or bring out the lube? How is that in there? WHY is in there? )
But then I think of Abrams as a Bay where you tell what the plot is. I don't like his work at all. It's all empty theatrics without anything real in it.
I have similar issues with his first attempt, which has things like "there was a lightning storm when I was born"... ehm, no, there wasn't? That was a black hole opening and since you've established that, there is no reason why that would happen again nor would nobody know the difference? If a movie doesn't even respect it's own rules, why should I?
(also how does that even work, lightning in space..)
And it just goes on like that. Also, it is sexist as fuck. Seriously, rewatch it with your current sentiments and put it next to the old movies. You're going to see time being reversed where apparently reboot future is the past.
Btw, Beyond is probably the first movie of all of them to have both the antagonist and major character be played by minorities (relative to the US being dominantly white that is). I'm not going to bother counting Klingons in I.D. since they're mostly there to be there for 'awesome white person Cumberbatch' to shoot them. For some reason. Couldn't imagine why that's in a script with sexism in it...
Beyond really should have come out in 2017, not the election year. It would have done better.
edit: oh, and I'm going to be the weird one to say that The Motion Picture, which really should be obvious by its massive cultural presence, is the best ST movie. Sure, Undiscovered Country and Khan are nice too, but The Motion Picture is equally as iconic as ALIEN was in the same year.
I think The Voyage Home is the most charming though. That's the easiest entry point into the series, while being self-aware about it. In hindsight, First Contact wanted to re-do that and the Borg at the same time which is tonally completely out of whack, whereas actual alien probe (why would aliens care about humans anyway?) is a far more legit plot device in Voyage.
So:
1: The Motion Picture
2: The Voyage Home
3: Wrath of Khan
4: Undiscovered Country
5: Beyond
6: First Contact (because schlock)
the rest is pretty much a wash.