It's highly likely that Apple rejected the app due to it being just a website wrapped in Phonegap/Cordova.
Probably your game looks and feels (UI/UX) does not conform to the iOS, have you used simulator to check weird issues in Xcode?
If there are no weird issues, perhaps you should implement 1 (one) native iOS feature such as notification, Geo-location, contacts, accelerometer, camera and and the like..
Please read the following documentation and apply any one of them to your game
http://docs.phonegap.com/en/4.0.0/cordo ... gin%20APIs
I think SplashScreen API would be enough
http://plugins.cordova.io/#/package/org ... lashscreen