Here's a few off the top of my head:
No touch interface support (full API in Flash, very early stages of development with HTML5)
No alpha channel support on top of video
No dynamic objects (captions / titles etc) or navigational items on top of video
Can't interact (e.g. record from) a webcam
Can't record audio from your microphone
Can't create desktop applications with HTML5
Very limited set of codecs (audio and video) in HTML5
No built in color correction
Can't handle binary data
No peer to peer support
No binary network sockets
No progressive streaming support (i.e. you can't jump into the middle of a video without downloading everything to that point)
No DRM support
No accessibility support
No Full Screen mode
In addition for most Flash games of any level of sophistication, recreating them in JS + HTML5 will be an incredibly painful experience for developers. AS3 has evolved into a robust, full featured language that well supports the needs of developers.