Incorporate the possibility of layers.
E.g. the same root node could have different children on different layers. [They could remain visible by having different levels of transparency (probably a max of 3 layers for clarity here?)] Thus the same root node could be explored in different contexts represented by the layers themselves.
One example (obviously users can create their own use-metaphors) might be that the root node represents a 'cause' with child nodes representing 'effects'. Different layers could show the effects of the root node "cause", given differing contexts- i.e. the cause has different effects in differing environments. However - effects common to different environments could colocate spatially so that you could easily see correspondencies and relationships.
Another application might be website mapping - relationships between pages in one section could exist on one level, whilst resources common to several levels (ie pages linked from several sections) might colocate over several layers.
All of which is to say that the visual metaphor of co-location is possible over layers: "something stays the same while other things change" - "something remains necessary whilst all around it differs", "something keeps occuring even when the circumstances have changed".
The possibility for confusion and obfuscation is of course a danger here, but used carefully, it might add something to the analysis of and integration of ideas.
I would love to use MindMUP for curriculum planning and having a "background layer" where an image could show swim lanes would awesome. This would be a features like Lucid Charts supports.
I like this idea...
I imaging this feature like... having a big mindmup and having assigned different nodes to different layers (each layer represents some metadata - concept), I could click and view only the nodes belonging to a special concept (preserving the relative node's positions).
I think that adding layers would be a great way to focus on the relationships between nodes. It's hard following every connection using the lines, but if tags were incorporated (another thing I'm hoping for soon) then all nodes and (connections between them) with the selected tag could show as a top layer.
Glen 06 commented
This could be implemented with the suggested metadata feature (http://mindmup.uservoice.com/forums/200447-what-should-we-focus-on-next-/suggestions/4593361-associating-metadata-with-nodes-to-enable-linear-s) and an ability to hide a node if the 'layer' property is set to some value.