It ain't over yet. Adobe are pushing hard into the higher end online browser based gaming market for PCs and Macs as well as pushing the same graphics and gaming capabilities for mobile devices through AIR and cross compiling (one code base - many platforms). The speed and agility with which developers can prototype games in Flash and the sheer number of skilled, experienced developers and a healthy vibrant community still makes it an ideal platform. In fact, some of the most popular and successful games on iOS are developed in Flash: http://gaming.adobe.com/showcase/ and distributed via iTunes instead of browsers.
Additionally, many of the popular graphics and physics engines and libraries for JS are being ported from AS 3.0, e.g. CreateJS and Box2D. HTML5+JS+CSS game development and mobile game development would be a lot slower without the support of Flash. Any Flash developer with experience of AS 2.0 will find coding in JS using the popular open source libraries ported from AS 3.0 to JS pretty easy. Flash is still enormously influential.
It's not that Apple don't want Flash, it's that they don't want competitors for iTunes. That's where they make a large share of their money. They're also doing their best to kill off second hand device markets by making batteries irreplaceable and parts unserviceable... which also makes them unrecycleable.