That bug is intractable with the current NPAPI and plugin vendor landscape. Slowly plugins are being replaced by web accessible technology. That is the way forward.
There are some things a user can do to avoid the issue as much as possible. Setting all plugins to ask to activate in about:addons resolves a number of common occurrences where plugins take focus on load. Set YouTube to use the 'HTML5' player [0]. Use pdf.js. If you are on OS X 10.7+ use Mozilla's Aurora branch to get h264 playback [1]. If you develop sites check for support of h264 playback instead of assuming Firefox does not have it.
There are some things a user can do to avoid the issue as much as possible. Setting all plugins to ask to activate in about:addons resolves a number of common occurrences where plugins take focus on load. Set YouTube to use the 'HTML5' player [0]. Use pdf.js. If you are on OS X 10.7+ use Mozilla's Aurora branch to get h264 playback [1]. If you develop sites check for support of h264 playback instead of assuming Firefox does not have it.
[0] https://www.youtube.com/html5 [1] https://aurora.mozilla.org