Well, it's true that JavaScript- and Canvas- powered ads are harder to distinguish from legitimate web content. But the flip-side is that they're (re-)programmable using standard JavaScript APIs, and thus vulnerable to manipulation by browser extensions in a way that Flash never was, being a proprietary binary format.
I don't have any trouble blacklisting domains for JS with current browser extensions. Why would it suddenly get more difficult?
They'll still be iframes or external scripts. Ads will always be trivial to block.
Yeah, HTML5 YouTube has the significant disadvantage of autoplay.
There's nothing preventing you from blocking HTML5-video just like Flash can be blocked with add-ons today. Personally I use NoScript for that.