I went through a bunch of diagraming options. draw.io is 2D diagraming only. There's also Lucidchart and few others. One other option seems to provide more than flat diagramming, but it's fixed to isometric projection (so, it is flat in the end).

I was also inspired by these diagrams from Amazon [1]. In Stackdraft, you press V key and toggle between 2D and 3D. You have full control over the point of view :). You can also create an animated presentation, like this one [2] - that one was just to show off a few AWS 3D models, so it's quite simplistic, but you get the idea :).

[1] https://aws.amazon.com/architecture/#aws-ref-arch

[2] https://twitter.com/stackdraft_io/status/1036557211554787331