Where Flash out-stands over HTML5 is games, presentations, ... lot of things HTML5 will never be able to do efficiently yet, and when that time comes, Flash will be miles away again. See for example Stage3D, tell me when HTML5 will be able to access the GPU directly.
Ever heard of WebGL? If you don't, google it! You know, that open specification from 9 months ago for GPU access implemented already in Chrome, Firefox, Safari and Opera?