This writing was on the wall for a looooong time, ever since Apple vs. Sun feud about Java.
… it is pretty easy to see why supporting other runtimes is ceding a lot of control to a 3rd party. Imagine if 10% of the apps on iPhone came from Flash. If that was the case, then ensuring Flash didn’t break release to release would be a big deal, much bigger than any other compatibility issues. [source]
Apple was there. They were maintaing Java compatibility themselves, making Mac OS X the best Java development platform and getting a bad rap for alway lagging behind the newest in java world. They clearly do not want the same with Flash or any other 3rd party crap.