They also take longer to start. More importantly they're impossible to control.

Came here to say the same thing. I have done a few extensive benchmarks internally and the conclusions were exactly the same (even though you don't need benchmarks really to know there is a difference). CSS transitions/animations have less overhead than Javascript ones. I think the issue here is perceived performance vs actual performance. People assume just because it looks fast and runs fast, that it is fast, when it in-fact comes with some overhead (that might not be visible on the surface).