While there are a couple of similar elements (you can rudimentary read and write data), the use case AppSync is trying to tackle is very different. It's main use case is not to act as the core of your application but rather as a wrapper around various AWS data sources.

There's a new concept called schema stitching which enables you to combine (and re-expose) GraphQL APIs which will make it possible to build a simple server that stitches together both Graphcool (as your primary data backend) and AppSync to easily access other information stored in AWS services. (You can read more about schema stitching here: https://www.advancedgraphql.com/content/schema-stitching)