Ilograph fulfills 2 out of 3: diagrams are broken up into a model (resources) and perspectives (their relations). The layout is always automatic, though. As a plus, though, this allows them to be interactive and dynamic.
Disclosure: I'm the dev
Tables are a pain, but most technical docs do not require rowspan and other things that are impossible to maintain in Markdown/reST/Asciidoc.
Diagrams are just a shitshow. PlantUML is the biggest player, and it tries to do the right thing by separating semantics and presentation, but kinda fails when your diagram grows too large.
I wish there was some tool that you could feed three separate human-readable inputs:
- styles, which let you define what your elements look like - semantics, which let you describe your elements and relationships - layout, which lets you manually rearrange the elements on your diagram (and is generated by a WYSIWYG tool)
Pikchr generates nice diagrams, but it's an all-in-one dialect. At least when I am reading well-written PlantUML I can understand the meaning of the diagram without seeing the rendered image.
The tool in the OP is nice, but it doesn't let you describe the layout at all.