We spent months searching for a multi-channel sales system, not only to replace Blackthorne, but to allow us to synchronize our inventory between eBay/Amazon and our own website. We tried BigCommerce and Volusion, as well as a handful of build your own API systems. All half baked. After spending thousands of dollars and countless hours trying to make something work, we finally stumbled upon SureDone.
Most everything is already there. A customizable shopping cart comes with the package or you can integrate one of the available 3rd party carts. Shipping systems built in or you can use plug-ins for ShipWorks. Payment gateway integration is turn-key. FULL eBay/Amazon integration. And if it's not there already, it's probably on the way. Customer support is top notch to boot!
If you want full multi-channel integration and can't spend $1000's+ per month, I can't recommend SureDone enough!