Those aren't the issues you talked about. Apple can't claim usability or accessibility as a reason for not adding Flash because a number of their apps and afaik, all their games, don't have any at all. It's not like the visually impaired have a braille version of the iphone that they can use to play Street Fighter 4 on.
We're talking about web masterpieces here. If usability, accessibility, and compatibility are your criteria, then Jakob Nielsen's site should be at the top of your list. So going by your criteria, here's your masterpiece: http://www.useit.com/
Now Apple's beef with Flash has supposedly everything to do with "performance", which we all know is utter rubbish. So using Apple's biased comments as a basis for an argument against Flash is weak.
The point I'm trying to make is: Let's not forget how much Flash pushed the web as a whole. The web went from ultra-static tabled pages with animated gif backgrounds to full blown "interactive media" sites. A lot of the early "masterpieces" were created in Flash, simply because Flash was, and most of the time still is, the best choice for a richer user experience.
A few of the classics:
Full interactive video site - afaik, this was one of the first, and still one of the best executed ones:
A site that gives a little extra if you have blue/red 3D glasses:
Barcinski and Jeanjean.com/
Online Promotional Game:
Coke Zero Online Game
A graphic classic: basically changed the way video game sites were designed:
2advanced (remember when this showed up? everyone went nuts)
A site that was always pushing stuff in subtle ways:
Leo Burnett (what used to be a pencil that drew along with your mouse gestures is now a 3D scene with reflections rendered in real time)
Playstaion-quality 3D graphics (basically proved that Flash can be used to build a proper 3D online video game)
Ecodazoo was built on this Roxik's Sharikura 3D engine
One of sharikura's recent examples (check out the real-time lighting and textures):
Let's not forget the countless other sites that used user-uploaded content such as video, on-screen graphics interacted with people through regular web cams, used sound as a basis for on-the-fly graphics generations, etc. etc.
The web we have today has taken tons of inspiration from Flash. Without that platform, we may still be building and designing gray boxes with full loading pages instead of the css/ajax-powered media sites we have now.