Nintendo has already said that Super Mario 3D All-Stars is going to be a limited-time release. Just how limited will it be? Comment from one retailer makes it seem like those interest in buying better make sure they get in on the item at launch.
A customer of Base.com had their pre-order for Super Mario 3D All-Stars cancelled, and it seems that all customers are in the same boat. In an email sent customers, Base has said that Nintendo and their UK distributors are unable to give reassurance that more stock will come after launch. That doesn't mean there's no chance at all for a restock, but it does make the situation iffy.
Again, if you want to lock down a physical copy for this game, make sure you do all you can to get one early on.