for example, it's much more efficient to let the browser (Safari) play html5 video and hardware decode it than the same video through flash.
it's also much easier to control things when it's not in a black box such as flash, browsers let you disable or whitelist things like JS, WebGL, etc.
To a developer Flash is not a black box - to a user, again - it seems that that technology gets a lot of blame for what developers are doing with it. If you have 5 animated banners hogging your CPU/GPU, whether in WebGL or Flash - who is to blame?
The blackbox comment is referring to it not being part of the DOM.
Of course the content of a plugin is not a part of the DOM - however you're not calling MP4 videos or webfonts "blackboxes" for not being able to read their source code from the web inspector either...
Playing SD quality video in HTML5 in Safari; minimal CPU usage, 7 hours battery life (on a 2012 MBA). Playing SD quality video in Flash in Safari; heavy CPU usage, audible fan noise, 2 hour battery life.
In a past life I did some Flash development; the Windows player was generally a little better (with the Mac one being in between and the Linux one being _horrendously_ inefficient), but it was still far from _good_.
Whitelisted/Click-to-play flash works relatively well.