I didn't find the movie the least bit complicated or convoluted. I mean I followed it as it was happening and it all made sense on the surface. That is what a good story does. Real life stories are usually flawlessly told, but they are also boring 99% of the time, that is why we enjoy the fake stuff.
Take any good or even great movie or TV show and look at it with a critical eye and you are going to poke giant holes in any story.
Star Trek itself is absolutely riddled with plot holes, inconsistent history, and bad science. I mean I guess its fun to discuss them from time to time because there is literally nothing else do with such big gaps between productions but I'd rather see someone not complain about a Star Trek movie for doing things done in other incarnations of Star Trek on a regular basis while still talking about how great those movies are.
I would say a criticism of acting and pace, and cgi is fine. But more often than not I am seeing a ton of complaints about things other Trek's have been doing for 50 years.