But CSS animations are...rough currently, not standardized, and don't have about a decade worth's of knowledge behind them. I can sure make a element fade in on a webpage with CSS, but there's already a billion ways to do it in JQuery on StackOverflow, so it's a lot more appealing to use Javascript at first.

I did not mention "css animations" in my post. Animations in general are certainly a common cause of website bloat, as they are often effected with a mix of images, javascript, and css which combine to waste bandwidth and cpu cycles. The article lists numerous sites for which animations contribute strongly to large website size. One such site listed in the article is this one: http://pollenlondon.com/ .