Many many many things, least of which is that it's not programmable. We can't set items that can go in flat rate boxes. We can't have "Free Shipping*" shipping, which is free shipping in the US and the equivalent discount in other countries, and other programmable shipping rates.
You're right in that I don't need a rate API, but Shopify needs a shipping API. Something where I can say "6 shirt or 4 shirts and a jacket is flat rate, but 2 shirts and a poster is not because of the tube"
