Why the Phase II Enterprise? Because it is a more modern design than the classic Connie. In the Abramsverse, the Enterprise is presented as brand new, the new flagship, whatever. In the novelization, it is written that the Enterprise is the culmination of all the data gathered by the Kelvin crew on the Narada. So here's my interpretation: the Enterprise already existed, but was called back from service a few years before this scene, and was thoroughly refitted, to the Phase II design. She was the testbed for the best tech Starfleet had, and thus the new flagship.
It's funny that you said the Enterprise already existed, especially since we find out in the Countdown into Darkness comics she was around, but she was retired when the new design came out.