One of our early adopters was a very notable/early Shopify customer who encountered the kind of problems you describe with templates and customization. I am pleased to say they have been successful using Forward and Shopify combined in order to solve these problems, and are planning to migrate completely when the time is right.
Shopify is a great solution for small business without irregular catalog and checkout requirements. I am however surprised that they haven't done more to support businesses that grow beyond this stage.
