Doesn't a 3D graphics (not game) engine like OGRE or Irrlicht fill this void? I don't know if either one supports DX12/Vulkan yet, but I imagine they will in the not too distant future.
I'm thinking more like bgfx, which is a cross platform API to access vertex and index buffers, textures, rendertargets, shaders and render states. Primitives like models, sprites, fonts, etc are up to you but the repo contains examples with extra utilities for those things.
Those are higher level scene graphs. D3D9 was an immediate mode API with some helper libraries, so you still were in control of your app's rendering architecture.