So I took a second look at the Galileo API (I pretty much haven't touched it since implementing it in one of the 1.x versions), and noticed there were a lot of warts to it that made it awkward to use or too rigid.  I came up with what I think is a more robust and usable design which will debut in minisphere 3.1.

The new API supports a transformation matrix per-Group, coordinates in 3D space (XYZ) as well as the ability to set uniforms for a Group's shader.  Here's the API documentation for what's in the git repo now:
https://github.com/fatcerberus/minisphere/blob/master/docs/sphere-api.txt#L729-L949

In theory it should also be possible to do basic 3D rendering by using a projection matrix, but I haven't tested that yet.  In any case it's not that far away from the original design as stolen from TurboSphere , but is much more flexible.

Could you update the pegasus spec while you experiment? So that the spec is always up to date?

I will, once I adapt the new stuff to my Sphere 2.0 fork.  What I showed above is the Sphere 1.x compatible API, so it needs to be adapted first.