With a fresh download of Cordova 2.9 and the Cordova CLI, I created Hello World application via the CLI. I also added the iOS platform via the CLI. Looking in the index.js file
The problem is because of the command line utility. There are two ways to create a project with the PhoneGap/Cordova CLI - Use the bash scripts that come with PhoneGap folder you download, and (2) to install the Cordova CLI.
I used the Cordova CLI, which doesn't use any resources you download, it downloads the latest release of PG - in this case 3.0, which isn't available yet on phonegap.com. It's very possible it may not be a stable release, because the console.log didn't work in the iOS app it created.
I tried using the batch script in the 2.9 folder I downloaded, and it created an app with fully functional console.log(ging).