These are good suggestions, and we have discussed adding some kind of grouping mechanism in Chimera given that there are a lot of situations where you want to treat a set of models as a single entity (e.g. multiple structures fit into a EM map).

I think #2 and #3 are in conflict though.  Really, I don't think you want #2 -- it's too confusing.  Say a model is in two groups:  you close one group -- what happens?  You hide one group -- what happens?  You deactivate one group and move the other -- what happens?  Perhaps if you elaborated on the motivation for putting a model in multiple groups then some other alternative could be devised that provides what you need.

I'll open a change-request in our Trac database for "grouping mechanism" and include the above.  I don't really want to promise a timeline, but the issue is a concern of ours.

--Eric