Silverlight 5 and WebGL offer hardware accelerated 3D graphics. So if you're making a new 3D game from scratch, SL or WebGL could be worth looking into.

If a company has no plans to use these premium features, then yes, I would imagine they will continue along as-is with Flash.

But a last thought; a revenue sharing plan like this will make big players nervous - what might Adobe starting charging for next? It will cause developers to start at least considering alternatives.