Just some searching, but seems that http://apiblog.youtube.com/2010/07/new-way-to-embed-youtube-videos.html method handles the determination of html5 or flash for the developer as part of the embed code. Maybe this method has accessibility issues as it is an iframe.
I used '<iframe class="youtube-player" type="text/html" width="640" height="385" src="'.$site.'youtube.com/embed/'.$url.'" frameborder="0">
</iframe>' in replace of the object code for the filter. However this failed to work on the iPod touch giving me a flash error.
From what I can tell the video embed tags for youtube require the user to be part of the beta program still. http://www.youtube.com/html5 That link details the information the additional restrictions seem pretty key.
I tested a video on iPod touch today from youtube using the object embed code and it worked fine, it didn't play inline it loaded the youtube app on the iPod touch.