JJ Abrams was the safest choice by Disney, His Star Trek reboot was phenomenal in that it respects the original crew but also brought new life to the franchise, a lot of people might disagree, but he done as well as anybody possibly could, and Into Darkness looks to be following that.
Saying that, I feels it's also a pretty boring choice, i'd have loved to see them go ballsy with the director choice, Matthew Vaughn was my choice, but director's like Matt Reeves, David Fincher, David O Russell, somebody who can bring a real edge to the franchise would have been exciting, I want it go nittier and grittier, it's got feel like Empire Strikes back the entire way through, where you just don't feel settled throughout.
It's in very safe hands, and they could have gone a lot worse (Brad Bird - Can't shoot Live-action sequences for toffee).