uhmm, I think you are looking at this backwards.. I could try and put 'zomg codec' on my site and play that via flash, flash would simply refuse to play it.. with the video tag, the browser would simply refuse to play it..
thats MY problem, as the site builder.. the video tag works the same way as flash, I really don't understand why its hard to understand because today if you want to play average codec 1.0 you need flash 9, if you want to use codec zomg super amazing brand new codec, you need flash 10..
With the video tag, if you want to play ogg/mp4 you need a video supporting browser.. if in 2 years time exists zomg super amazing brand new codec, you need the latest versions of the browser..
Lets look at the event I want to use zomg super amazing codec with flash, someone hits my site and oops, they don't have flash 10, all I can do is tell them they need to update flash.
In the web scenario I use zomgsuper amazing codec, and the user doesn't have the latest version of their browser, then all I can do is tell them they need to update their browser.
The reality is the same, if you want to use technology x, you need to discover just how many of your audience will have technology x, or more importantly, how many won't have technology x, and in that case, is that a risk I want to take, do I really want to disrupt THAT many users experience with a 'you need to update something', and how many of those will say 'forget it'..
Theres nothing intrinsically faulty with the design of video in this regard, any 'document orientated' technology where you only send the document and expect the client has something installed to understand that document to get a result will always have this flaw.