Stacks should be handled uniformly, regardless of the source selected. As it stands, stacks are second-class citizens in Lightroom.
* Currently, photos in different folders can’t be stacked. This restriction forces users to be aware of which folder a photo resides in, which goes against the mainstream digital-asset-management philosophy of hiding folder locations. I don’t know of any use-case justifying this restriction.
* Stacking isn’t displayed when viewing collections and smart collections. This is especially annoying when viewing smart collections, since smart collections are the only way to do advanced searching. It would be better if stacks were viewable within collections just as they are within folders and with filtering – when more than one photo in a stack is part of a collection, then the stack could be collapsed or expanded, but only the photos in the collection will be shown. This is the way stacks work now with filtering, so extending this to collections would be consistent. Users who don’t want to see stacking in collections could simply invoke Expand All Stacks.
* And of course, you should be able to stack and unstack photos when viewing a collection.