It seems to me that in the process of creating ‘Variations’ instead of a distinct type of listing being created variations is just another type of product ‘option’ with the same kinds of limitations.
For example it would be more logical to me if ‘variations’ had a group listing umbrella that covered all the variations instead of the group listing primary simply being another variation.
e.g. If I create a primary listing for Patent Leather Shoe and then variations of Brown, Black, Blue I end up with 4 listing variations instead of just 3 variations (Patent Leather Shoe, Brown, Black, Blue), if I changed the primary listing to Brown then I end up with 3 listings without adequate grouping of the listing.
In functionality this seems hardly any difference to creating a listing with options and tracking options.
The other problem with the lack of a listing umbrella is that you cannot specify minimum quantities for the listing group you can only specify minimum quantities for each variation which makes no sense for a group of products. e.g. If I wanted to specify a minimum quantity of 2 pairs of shoes of any variation or option this does not seem to be possible as the customer then needs to purchase 2 pairs of each variation or option.
Same problem with quantity discounts, if you set a quantity discount for 5 items within a product group with variations a customer would naturally assume that if they purchased 5 different variations then they would get the discount not that they need to purchase a quantity of 5 of each variation to get the discount.
If variations had been created with (Group Listing) > Select your Variation and the product listing was treated as an actual group with minimum quantities for the group then variations would have been a completely distinct type of product listing as compared to options.