Full screen videos in Chrome suffer a lag
If I've understood the video correctly, it's the long animation you're wondering what is? I don't see any other lag, please do correct me if I'm wrong.

Using the HTML5-version of YouTube, utilizes OS X's built in full screen mode. The animation from single-window to full screen in OS X is this slow, and it annoys me as well. Try disabling the HTML5-mode from here, or to shorten and/or remove the full screen animation it alltogether, see this question and it's answers.