I will thank Microsoft later for this curve ball. As many of you might know, Exchange 201x only supported up to .NET 4.5.2. Recently 4.6.1 had been released and has even been added to the Windows Updates. If you are pulling updates automatically to your Exchange Servers (something I would never recommend), then you may want to consider changing that process. A .NET update on an Exchange Server is not something you just want to happen because if you are running Exchange 2013 CU12 and before or Exchange 2016 RTM / CU1, a .NET upgrade could bring you some potential headaches.
.NET 4.6.1 Support Added
Those headaches will hopefully go away with the new CU releases for Exchange Server 2013 and 2016. Exchange 2013 CU13 and Exchange 2016 CU2 now support .NET 4.6.1. The caveat is that you need to upgrade the Exchange Server FIRST and then you can update .NET to .4.6.1. If you attempt the reverse, then you will need to uninstall .NET 4.6.1. A fellow Exchange MVP and Exchange Master, Jeff Guillet has written a great article on that process and covers any pitfalls you may run into – here.
While installing .NET 4.6.1 for the first time, the upgrade stopped and a pop-up box notified me that the server was missing an update for the Windows 2012 R2 OS that is apparently a prerequisite for installing .NET 4.6.1 on the server. This update does not get installed by default on a fully patched Windows 2012 R2 server (direct from Windows update built into the OS). The update in question is https://support.microsoft.com/en-us/kb/2919355. While experimenting with this update in order to update my Pre-Requisite scripts I use for Exchange 2016 and Exchange 2013, I noticed that the installation takes literally forever. I even used a stop watch for one install in a lab that took approximately 25 minutes. I tried to build in a silent installation, but was unable to and ended up with the script starting the install and then you need to tell the program to install. While the hotfix is installing the script informs you of the wait. A couple of additional informational lines were added which tell you to reboot after the hot fix is installed, after reboot to re-run the script and choose option 21 once more for .NET 4.6.1.

Again, make sure to do this AFTER installing the latest updates for Exchange server and not before.
The newly updated script for Exchange Server 2016 is up on the TechNet Gallery:
Exchange Server 2016 Prerequisites 1.4.
The updated Exchange Server 2013 script will be coming in the next few days as I test the updates and the script to install .NET 4.6.1.
NOTES
The current script will install .NET 4.6.1, but apparently there is a hotfix that needs to be applied post .NET install. Look for the prereq. script update by Monday of next week.
https://blogs.technet.microsoft.com/exchange/2016/06/21/released-june-2016-quarterly-exchange-updates/
Excellent post. Please keep up the great work.