Into Darkness was alright. Certainly better than the first one, but still pretty flawed. Making BC Khan was silly. He/it would have been much better as a generic pissed off dude. Almost all of the throwback references to TWoK were stupid as hell. The blonde girl, while cute, was pretty much just eye-candy and a convenient plot device. Also, they could have turned 20 minutes of action sequences into character development and exposition and still had plenty of excitement left. That said, there was some good humor and the story wasn't bad. The special effects were much less chaotic than the first one, so you could actually tell who's shooting at what most of the time; big improvement. All in all, it wasn't bad. It's still not Star Trek, though.
And I'd give pretty good odds that The Borg are involved somehow in the third movie. I'd almost guarantee it.