When configuring a Windows Routing and Remote Access Service (RRAS) server to support Internet Key Exchange version 2 (IKEv2) VPN connections, it is essential for the administrator to define the root certification authority for which to accept IPsec security associations (SAs). Without defining this setting, the VPN server will accept a device certificate issued by any root certification authority defined in the Trusted Root Certification Authorities store. Details about configuring IKEv2 security and defining the root certification authority can be found here.
Multiple Root Certificates
Administrators may find that when they try to define a specific root certification authority, the setting may not be implemented as expected. This commonly occurs when there is more than one root certificate in the Trusted Root Certification Authorities store for the same PKI.
Certificate Selection
When running the PowerShell command Set-VpnAuthProtocol to define the root certification authority, PowerShell may ignore the administrator-defined certificate and choose a different one, as shown here. This will result in failed IPsec VPN connections from Windows 10 Always On VPN clients using IKEv2.
Certificate Publishing
This issue can occur when root certification authority certificates are published using Active Directory group policy. It appears that Windows prefers Active Directory group policy published certificates over those published directly in the Certification Authorities Container in Active Directory. To resolve this issue, remove any group policy objects that are publishing root certification authority certificates and ensure those root certificates are published in the Certification Authorities container in Active Directory.
PowerShell Script
A PowerShell script to configure this setting that can be found in my Always On VPN GitHub repository here. I have updated this script to validate the defined root certification authority certificate and warn the user if it does not match.
Additional Information
Set-Ikev2VpnRootCertificate.ps1 PowerShell script on GitHub
Windows 10 Always On VPN IKEv2 Security Configuration
Windows 10 Always On VPN IKEv2 Load Balancing and NAT
Windows 10 Always On VPN IKEv2 Features and Limitations
Microsoft recently made available an update for Windows 10 2004 that includes many important fixes for outstanding issues with Windows 10 Always On VPN. 
Microsoft 
During the planning phase of a Windows 10 Always On VPN implementation the administrator must decide between two tunneling options for VPN client traffic – split tunneling or force tunneling. When split tunneling is configured, only traffic for the on-premises network is routed over the VPN tunnel. Everything else is sent directly to the Internet. With force tunneling, all client traffic, including Internet traffic, is routed over the VPN tunnel. There’s been much discussion recently on this topic, and this article serves to outline the advantages and disadvantages for both tunneling methods.
Recently I wrote about 
NetMotion Software and Microsoft have now partnered to integrate NetMotion Mobility with Microsoft Endpoint Manager and Intune. NetMotion Mobility is a purpose-built enterprise VPN solution that has many advantages over competing remote access technologies. Using Microsoft Endpoint Manager or Intune, organizations can now quickly and easily provision NetMotion client software to their managed devices.
The Internet Key Exchange version 2 (IKEv2) VPN protocol is the protocol of choice when the highest level of security is required for Always On VPN connections. It uses IPsec and features configurable security parameters that allow administrators to adjust policies to meet their specific security requirements. 
