I mean, CSS animations are cool, but CSS3 compliance is annoyingly un-standard. but, ignoring all the issues with browsers and their inability to be up-to-date with the late
CSS animations can be accelerated by the GPU, whereas Javascript animations aren't. If You know without a doubt that your user base will have support for the css version of your animations, it makes a lot of sense to choose css.
In the case that you need to support older browsers, javascript is the right call.