For the most part runtime treats shapefiles as a readonly source. It would allow you to read existing ones, but there isn't currently anything within the API to allow you to create new ones or edit existing ones. That being said, it isn't entirely impossible to create shapefiles with the current runtime API if you leverage ArcGIS Server or Local Server.
If you have access to ArcGIS Server and your users are in a connected environment you could create any data structure (i.e. shapefiles, file geodatabases, etc.) that you can create in ArcGIS Server. You'd just need to return this data as a zip file from the server and unpack it on the client. On the other hand, I've been able to accomplish this using LocalServer for disconnected workflows in Runtime for .NET. I would assume that because LocalServer is essentially the same between between Java and .NET that these workflows would work there as well.
To create the tool you could do something as simple as running the copy features tool in ArcGIS Desktop. The output of this tool would need to be a shapefile. You could then publish this tool to ArcGIS Server or a Geoprocessing package (gpk) and you could leverage this from runtime to create your shapefiles.
Let me know if this makes sense.
