It'd be kinda neat if you could have multiple user layers in a single style with a precedence order. Users could then mix and match different kinds of tweaks for different galleries without the “convert user layer to theme” kludge. The S2 backend can handle this already, but the database schema and the interface enforce only one of each kind of layer.
It'd involve adding a field to the style table to number several of the kind of layer so that more than one user layer can be referenced, and the interface would require multiple select boxes where the user can select “None” or any user layer they have up to some arbitrary limit. This clutters the interface, which is a disadvantage.