I am moving my website from webapp to a hybrid app (to get it on the app store). The webapp uses js, jQuery, and Kendo UI for logic. Apart from added features that will be accessing native APIs on the phone that obviously aren't on the webapp, what main changes should I be on the lookout for.
I guess another way of asking this question is, in technical sense, what are the main difference between the code for a webapp and the code for a hybrid app coded in PhoneGap?
Having looked into this myself, the biggest thing that you will face when it comes to attempting to get an App into the AppStore, is the User Interface.
Apple is very strict about their user interface guidelines, so a Hybrid app that doesn't look like a native app is likely to get rejected. In addition, since they are quite strict about their user interface guidelines, if you can change the user interface after approval (say, because your app just mirrors a webpage), they will likely reject you coming in.
Andrew Trice of Adobe (makers of PhoneGap) has some great advice in "PhoneGap advice on dealing with Apple application rejections".
He goes into a good amount of detail, but the big 3 things he points out that apps need to avoid rejection are: