I have a few solutions with many assortments (eventually up to maybe a few hundred). Currently, they are all listed as one long list:
Can you add an option to categorize them? In its simplest form it could be like how item types are categorized with just a category field on the edit screen. But it might also be nice to have a bit more smarts on the categories so the assortments are lazy-loaded for each category. Currently, with that many assortments, opening up the Ecommerce node is pretty slow, presumably because it's loading all assortments data at that point. Loading by category may solve that problem as well.