This is one of the frequent query which i come across. whenever i talked to my app developer customers community. They wanted to know whether they should be using Microsoft Graph (developer.microsoft.com/graph) or Azure AD Graph (graph.windows.net); also i see good number of discussion threads talking the same. In order to conclude this and provide guidance/roadmap, Dan published this wonderful article. I would recommend to have a look at that before you start developing. Please refer https://dev.office.com/blogs/microsoft-graph-or-azure-ad-graph
In general, we recommend the use of Microsoft Graph over Azure AD Graph, as Microsoft Graph is where we are investing for Microsoft cloud services.