I'm not sure about multiple inventories, but I would like to see a sub, perhaps 'collection' within inventory. My scenario is that myself and close friends would frequently buy boxes and would like enter those in to easily see the 'money' cards, box value and such and then initiate trades on that lot alone. As it stands, we need to add them as a new deck which can be a little restrictive. We cannot mark one as foil or edition for example and it is not counted in the inventory until print/import.
Additionally it could be used to house 'blocks' and although this can be done with filters, it just seems like it would fit quite naturally into the site.