I have repeatedly had clients on a budget choose Magento over Shopify due to a lack of fine grain control. It's very frustrating that they can release a POS system, however fail at, for example, complex sales reports. I wish they'd get it together because they would blow everyone out the water.
Their shipping options completely suck for anything but trivial sales, too, unless it has changed in the last month or two. (Example: most products are free shipping but a few large products are not free; there was no control to exempt products from free shipping, nor any control to say products were not eligible for certain shipping methods. Not all merchants can overnight a 50kg box, for example.)
If that's not good enough there's apps like Better Shipping that can set up more complex shipping rules - http://apps.shopify.com/better-shipping