The article basically says, make good games, which really has nothing to do with the tech of HTML5. I've had a few of my titles featured by Apple and I am often asked what I did to get them to notice my title. The answer is extremely simple: "make good games".
But yeah, audio is a big problem. I'd argue that caching and content distribution in general are probably the other big problem. Having to roll your own complete solution for downloading and caching assets for every game is a pretty big problem, in part because the available options for storing assets on a client are pretty miserable in HTML5.
Flash was brought up because it was a huge delivery mechanism for a huge portion of casual games over a significant time period. The general theme of the article is that because HTML5 is the up-and-coming technology in the casual games area, many games miss out on basic strategies employed by games on more less cutting-edge platforms.