First make sure your existing Exchange Servers are patched to at least CU10.

Disk requirements:
60GB OS Disk (NTFS),
60GB Exchange install disk (NTFS),
30GB Exchange database (ReFS),
5GB Exchange logs (ReFS)

For ReFS file systems, disable integrity bit:
Get-Disk 2 | New-Partition -UseMaximumSize -DriveLetter F | Format-Volume -FileSystem REFS -NewFileSystemLabel Exchange_Database -SetIntegrityStreams $false
Get-Disk 3 | New-Partition -UseMaximumSize -DriveLetter G | Format-Volume -FileSystem REFS -NewFileSystemLabel Exchange_Logs -SetIntegrityStreams $false

Post-deployment of Windows Server 2012 R2:
Install VMWare Tools
Configure a static IP
Name and join the server to the domain
Prepare and format the additional disks
Apply Windows Updates
Enable Remote Desktop (optional)

Install the Windows Feature prerequisites

Install-WindowsFeature AS-HTTP-Activation, Desktop-Experience, NET-Framework-45-Features, RPC-over-HTTP-proxy, RSAT-Clustering, RSAT-Clustering-CmdInterface, RSAT-Clustering-Mgmt, RSAT-Clustering-PowerShell, Web-Mgmt-Console, WAS-Process-Model, Web-Asp-Net45, Web-Basic-Auth, Web-Client-Auth, Web-Digest-Auth, Web-Dir-Browsing, Web-Dyn-Compression, Web-Http-Errors, Web-Http-Logging, Web-Http-Redirect, Web-Http-Tracing, Web-ISAPI-Ext, Web-ISAPI-Filter, Web-Lgcy-Mgmt-Console, Web-Metabase, Web-Mgmt-Console, Web-Mgmt-Service, Web-Net-Ext45, Web-Request-Monitor, Web-Server, Web-Stat-Compression, Web-Static-Content, Web-Windows-Auth, Web-WMI, Windows-Identity-Foundation

Download and install these components:
.NET Framework 4.5.2
Unified Communications Managed API (UCMA) 4.0

Install the RSAT Active Directory tools
Install-WindowsFeature RSAT-ADDS

Prepare Active Directory for Exchange 2016

Note: Perform this step on a DC in the same site and domain as the schema master FSMO role (Run netdom query fsmo in CMD to find out where the Schema Master FSMO role is), with an Administrative account that has both Enterprise Admin and Schema Admin privileges.
Update Active Directory Schema to the new 2016 attributes:
Setup.exe /PrepareSchema /IAcceptExchangeServerLicenseTerms

Note: Perform this step on a DC in the same site and domain as the Schema Master, and with Enterprise Admin group credentials.
Prepare the existing Exchange Organisation for 2016:
Setup.exe /PrepareAD /IAcceptExchangeServerLicenseTerms

Note: This command prepares all domains in your forest and requires Enterprise Admin credentials.
Prepare all domains:
Setup.exe /PrepareAllDomains /IAcceptExchangeServerLicenseTerms
Note: This command prepares a single domain and requires Domain Admin credentials for the specified domain. Run this in each domain you want to host Exchange on.
Prepare individual domains:
Setup.exe /PrepareDomain:<FQDN of Domain> /IAcceptExchangeServerLicenseTerms

Installing Exchange 2016:
Installing via the GUI:

  1. Launch SETUP.EXE from the iso:
  2. Click next at the Check for Updates prompt, click next again after the check.
  3. Click next on the Introduction page and Accept the License Agreement and click next again.
  4. Choose Use recommended settings, click next.
  5. Select Mailbox role and Automatically install Windows Server roles and features that are required to install Exchange Server
  6. Select the Installation Space and Location (In my case it's the Exchange Install, E drive). Click next.
  7. Select Yes for malware scanning, click next.
  8. If the readiness check is successful, click Install otherwise troubleshoot the cause and click Retry. Exchange will now install.
  9. Click Finish and reboot.
  10. Once rebooted use the URL https://servername/ecp to administer the new server.

Or, alternatively install via Powershell:

  1. CD to the iso from Powershell
  2. Run this command: Setup.exe /Mode:Install /Role:Mailbox /TargetDir:"E:\Exchange Server\V15" /InstallWindowsComponents /IAcceptExchangeServerLicenseTerms
  3. You will see the progress via the Powershell, once completed you should see an output which shows you all the installation steps and the status (COMPLETED or FAILED).