Click-to-play doesn't let you disable it temporarily, which is a problem for some sites that rely on background Flash files. On Chrome, I prefer https://chrome.google.com/extensions/detail/gofhjkjmkpinhpoi...

I'm not sure I understand your meaning. Using just click to play in about:flags, on a page with blocked plugins you can click the icon which appears next to the bookmark star and select "Run all plug-ins this time". Is that not sufficient?

Ugh, I honestly hadn't noticed that. Maybe it wasn't enabled yet on the dev build or something.

Still, per-site whitelisting is nice.

For per-site whitelisting, you can click on that icon and check "always allow plugin on ..." or go to "settings > under the hood > content > plugins > manage exception."

It isn't the easiest or most intuitive way, but so far worked well enough to me.

I am not 100% sure if that extension is totally blocking the Flash files. Last time I checked it, it was only applying a "display: none" with CSS, and some files slipped past it, making it ineffective against 0-day exploits.