Since TwentyTwelve will serve as a best practice example for Theme Developers, I would be thrilled if we could move all scripts and styles to functions.php, to adhere to this guideline in the Theme Review process.
From what I understand, leaving the comment-reply script in header.php is technically still acceptable, but let's set a good example! :)
Maybe, to top it off, we could add a comment to that html5.js script in header.php, explaining that scripts wrapped in conditionals there, are okay.
Move scripts and styles to functions.php and enqueue them there properly
Enqueue scripts and styles properly and namespace them, to serve as a…
… best practice example for Theme developers
Thanks for this and your other two pull requests.
We discussed this already in core, see Nacin's comment here: http://core.trac.wordpress.org/ticket/19978#comment:4
I agree we should keep it in header.php for simplicity.
Also, a side note: default theme names have a space between "Twenty" and the number. (Twenty Twelve, not TwentyTwelve.) :)
Thank you for your consideration, Lance!
I hope I'll get the chance to contribute in the future. :)