(Not using the WiFi enabled version of the board.)
In my case I kept finding that the all-important Blink example from the code out there on Github wasn't being allowed to deliver and debug to the chosen Netduino3 who's the Ethernet version. This was also on VS2015. It was the Community edition if it helps.
It got stranger than fiction from there, I also snagged some of the VS2013 tools, and installed and tried that. It kept complaining that the properties file was in a format that it didn't understand.
I then did a fallback and installed good old VS2012 and tried that out. And it worked.
Mark what's involved in getting even the simplest program delivered to the device when running VS2015?
Incidentally this is all on a brand new laptop as of Wednesday, my previous one officially shut itself down for good towards the tail end of January and I needed to spend the time tracking down a new guy.
And this message is being sponsored by the fans of Dwarf Grumpy.