I've only seen Beyond once right now due to ticket prices and the horrible projection quality at our local cinema, but as much as I enjoyed it, it just didn't give me as much to think about as the previous two.
The first movie had a simple story but was a really satisfying experience that left you thinking about the whole new universe of possibilities it created.
The second one slight wasted that by using Khan but made up for it by telling a complex story with actual themes and moral issues. When I walked out I didn't feel satisfied in the same way as ST09, not because it was bad, but because I felt like immediately watching the next episode in the TV series that this should have been.
Beyond had some really good moments and lines, and Jaylah is probably the best character created for a Star Trek movie in a long time, but it just felt like it was lacking something. Maybe part of it was the destruction of the Enterprise (in the anniversary movie, the Enterprise should not be treated as a redshirt) but mostly I think it's the thinness of the plot. STID, ST09, and NEM were all criticized for being about a madman wanting revenge, and both Pegg and Lin promised to do something different, until the last 15 minutes of the movie were Krall turns out to be a madman wanting revenge, and for a much weaker reason than Khan or Nero. And then what did Kirk learn from the experience? His arc is basically "I'm old and space is boring. All I do is get my uniform eaten by space monkeys, I should quit and get a desk job instead. Oh wait, my ship is destroyed, most of my crew is dead and a psycho tried to melt me. Why would I want to give this up?" Compare that to the previous movies where we first see Kirk go from loser to hero, which makes him overconfident, and then to a capable leader.
I know this may feel like Beyond-bashing, but I did genuinely like the movie. I just feel that the previous movies (STID in particular) had more substance and were more interesting and this is the reason for STID having higher critical scores.