-Previous installed chrome app matches the HTML5 api, the new chrome apps has a lot of restriction where you have to totally rewrite you code in terms of storage. i.e. Chrome.storage instead of localStorage; All chrome storage is async.
-The new window format for apps are a huge UI flaw. You can not open an Chrome app in a tab anymore. Basically, you now have an extra window whenever you open a chrome app. This is very annoying since when you click on the existing window the app is hidden in the back, you have to flip through your windows on the mac to find the app you just opened again.
-Javascript execution permissions are very strict, and no longer follows that of a normal webpage.
The result is, you can no longer build an HTML5 app and prepare it for the chrome store, you have to specifically change the code to package it. This makes it less ubiquitous and creates extra work for developers.