Even if it all gets buried under high-level visualisations, it's better to have fewer moving parts and a smaller cognitive model in case you do need to dive in. But the premise of d3 is that you tweak your visualisations. There are other libraries like raphael that are supposed to be higher level.

But there are many times you need to create something new. At least I've had to, maybe I'm atypical. And when that time comes, I prefer manipulating familiar HTML and AngularJS that I also already know, than needing to understand yet another toolkit's approach to bindings.