Recently I read the book by Kent Weare which talks the difference between WCF-SAP Adapter vs WCF Custom Adapter with SAP bindings.  

WCF Custom Adapter with SAP bindings

Once you use Consumer Adapter Service (Add—Add Generated Items…Consume Adapter Service) by passing SAP Connection details it generates binding file along with schemas. While configuring WCF-Custom adapter for the sapBinding , we can manipulate any SAP-related property. Here to configure the WCF-Custom Adapter, you need provide SAP connection string. For example sap://CLIENT=100;LANG=EN;@a/sv-sap-dv1/00?GWHOST=sv-sap-dv1&GWSERV=sapgw00&ListenerProgramId=BIZTALKDEV&RfcSdkTrace=False&AbapDebug=False The Address (URI), which is the  SAP connection string can be confusing at times and one minor mistake will result in an error.  

WCF-SAP Adapter

WCF-SAP adapter is comparatively easy to configure than SAP URI.  By clicking the Configure button, we have the pop up to provide all the key details (like Gateway Host, Gateway Service, Program Id etc.. )  for a SAP connection. To create a WCF-SAP adapter, you can refer Add adapters to BizTalk Administration Console section of  BizTalk Server 2013 R2: WCF-SAP Adapter Step-by-Step Installation Guide published by  Sandro Pereira.

Conclusion

So in conclusion it really does not matter whether you use the WCF-Custom Adapter or WCF-SAP Adapter, because you are not losing any functionality. Using the WCF-SAP adapter does simplifies the administration tasks that are involved in maintaining our BizTalk environment.

Resource:

Microsoft BizTalk 2010: Line of Business Systems Integration

Related links:

http://social.technet.microsoft.com/wiki/contents/articles/13150.biztalk-server-wcf-based-sap-adapter-and-troubleshooting.aspx