I honestly have tried both and have to say both of them are equally as good. It boils down to personal preference. In the past few months I have helped a few friends set up their shopping carts and went with Shopify because their Affiliate commission.

If you do decide to go with Shopify be sure to check out their 4th Build a business competition http://www.youtube.com/watch?v=zZciwQ6ZlsY