I do realize flash/java are behind on OS X, and if Job's believes they need to be outmoded, then by all means do it, he's far more qualified than I am to make calls like that so I trust his judgment- but there should be something in place to bring rich web content to OS X in their absence. Did you know that there are full-blown 3D games that run in web-browsers? (Garage Games), also government funded "flash based" assistance programs, such as those for foster children, that are supposed to have a 20 year shelf life.
I don't have any problems whatsoever with Apple's decisions, I use only Mac's and Apple gadgets at home, however 2 things:
1. It is about control and money, always is. These exclusions are probably part of laying the ground work for The Mac Store.
2. Replace Flash and Java with something that is widely accepted by the development community, note: acceptance is key. I've heard of HTML 5, but I've only seen a few examples of it, a shooter game and video playback on youtube. (*** sorry I'm out of touch with this issue, html 5 may already be more prevalent than I realize, if that's the case then this is a moot point.)