Using SQL Server 2016 R Services over a standalone installation of Microsoft R Server
Possible a slightly subjective question but sometimes it's helpful to think of these things in scenarios, for example:


A predominantly SQL Server project, run by DBAs/devs (who may or may not know some R).  A data scientist or R professional writes some R for them or they do it themselves and test on their local machines, eg using R Studio or the Microsoft R IDE.  When they are happy with the R, they plug it into their data workflow using sp_execute_external_script.  They can easily incorporate this into other stored procedures, SSIS etc.  This might be a good candidate for SQL Server 2016 with R Services.
A secure project, the data is in your secured SQL Server and you want to keep the data close to the analytics and not use the cloud.  This might be a good candidate for an on-premise installation of SQL Server 2016 with R Services.  
A predominantly data science project which requires data but does not require SQL Server access.  This might be a good candidate for Microsoft R Server only.
High performance is required for a big data project.  You do not want to share the box with the traditionally memory-hungry SQL Server.  This might be a good candidate for Microsoft R Server only.


Just a few examples there.  What examples can you think of?

HTH