Why didn't Wired use HTML5?
1) a) it was built by Adobe who build it on Flash to begin with, b) the tools just aren't there yet. c) because of #2.
2) Why is the app 500MB? Because all the rich content (images, movies, audio) are bundled into the app so you do not need an internet connection to view it. I think we can all agree that downloading a "magazine" before you leave the house, then finding you can't view most of it, would be an uber fail.
If the app had been based on HTML5 it would have been a 'mare to cache all of the content locally for offline viewing. HTML5 does offer local storage, but not in a way that would allow sites to cache 500MB of content. And even if they could, do you really want to wait 20 minutes for that Pixar feature to download over 3G?
I suppose you could have created a native app with everything bundled locally and a UIWebView for rendering the HTML5 content, but really what do you gain from that?