@se7enhedd: If you name some geo in the AE, you'll notice that if you rename the transform node, it will rename the shapeNode for you, kinda useful. In the outliner, the transform node is the upper level node, so it can be renamed there as well. If you rename the shape node, it won't update the transform node name, I think because of the directional connection. Hope that makes some sense, it might just be arbitrary, I don't know.
@bullet: I don't really use the hypergraph much yet either, but it's something I'd like to focus on more. I think they don't have a one-for-all cause it would be super overwhelming and not really as useful.