After getting my Netduino3, I was able to create a program using VS2013 with the Netduino Universal template.
There was an initial compile error caused by the missing .NET 2,3.5 etc. Framework. Installed those and everything compiled fine.
When I first tried to start debugging, it gave a "deployment failed" with no error codes. So, I compiled a release version and deployed it without debugging. That worked fine. The next time I tried to start debugging it worked fine. Don't know if had anything to do with the previous deploy.
But, everything is happy now!
I'm using VS2015 for Rasberry PI Windows 10 IoT development. Probably just keep using VS2013 for Netduino.