Is this a brand new VM or one that you have had for a while?
I ask because I spun up a new 2016 machine to see if I could repro the issue but it looks like .NET 3.5 installed without issue:

This leads me to believe that something might have happened during the provisioning of this VM that caused the dependencies to be missing.
Couple of things you could try:
1) If this is a brand new VM try simply spinning up a new one and installing .Net 3.5. If it succeeds just use that machine
2) You could create a second 2016 machine and attempt to copy the dependencies from that new machine over to your old machine
3) Download the .ISO for Windows Server 2016, Mount the .ISO as a drive and copy the /source/sxs folder to where you need it.
-Micah