Are you only using the embeddable player with all the controls included? I just started using YouTube's HTML5 player as a fallback for users who don't have Flash, but with a chromeless player and using their iFrame API. The iFrame API is definitely rough on the edges, but it is experimental. And as far as I know, the HTML5 player for YouTube is in trial so I'd give them the benefit of the doubt on bugs and that they're working on it.

I haven't seen the bugs you mentioned, but will look out for them now.