I think the movie tried too hard to have its cake and eat it too.
It's trying to reinvent the franchise with its own vision, but it's also leaning on fan memory of the old movies to establish its themes.
Take Khan. Pretend the original series didn't exist, this is just a new movie in a new franchise. So you have no idea how dangerous Khan was from the original series. Based only on this movie, how scared are you of Khan? He seems like a pretty bad guy, and an unfeeling sociopath. But on his own, separated from his resources do you really feel like he's the greatest threat the galaxy has ever known?
The movie did not work very hard to establish Khan as a threat, it leaned on the fans' memory of Wrath of Khan, and the fans' memory of the scenes it directly reproduced from Wrath Of Khan. Which is something you don't get to do if you're completely changing the series.