Cytoscape WikiIliana: Here is my opinion on each of the proposed data structures:
CyAttributes Requires that a node (if we use node CyAttributes) or an edge (if we use edge CyAttributes) be created per group. Only in one case (COLLAPSING_STRATEGY) is a node per group needed. The other grouping strategies do not need new nodes or edges. Additionally, there is no safe way of storing information that tells us to which network a group belongs, since the node that functions as a key in CyAttributes can be manipulated very easily by users (removing it, adding it to a new network, etc).
CyNode Also requires a node per group. This was originally done because when we were designing the GINY API, we were not thinking of the more general grouping problem. We were thinking of MetaNodes only.
A new data structure. This could be a data-structure that resembles CyAttributes (some sort of map structure) but that does not require the creation of a node per group. Also, this data structure would be hidden, so that the only way of interacting with it is GroupingManager. I vote for this.