WIX has NetFxExtension with NetFx4XXXX packages, so .NET Framework 4.6, for example, can be installed with the single line of code:
<?xml version="1.0" encoding="UTF-8"?>
<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi" xmlns:bal="http://schemas.microsoft.com/wix/BalExtension" xmlns:netfx="http://schemas.microsoft.com/wix/NetFxExtension">
<Bundle Name="My App">
...
<BootstrapperApplicationRef Id="ManagedBootstrapperApplicationHost">
<Payload SourceFile="$(var.MySetupUI.TargetPath)"/>
<Payload SourceFile="$(var.MySetupUI.TargetPath).config"/>
<Payload SourceFile="$(var.MySetupUI.TargetDir)BootstrapperCore.dll"/>
<Payload SourceFile="$(var.MySetupUI.TargetDir)BootstrapperCore.xml"/>
<Payload SourceFile="BootstrapperCore.config"/>
<Payload SourceFile="C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.5\System.ServiceProcess.dll"/>
<Payload SourceFile="C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.5\System.Configuration.Install.dll"/>
<Payload SourceFile="C:\Program Files (x86)\WiX Toolset v3.11\SDK\Microsoft.Deployment.WindowsInstaller.dll"/>
</BootstrapperApplicationRef>
<Chain>
<PackageGroupRef Id='NetFx46Web'/>
<MsiPackage SourceFile="$(var.MyAppSetup.TargetPath)" Id="InstallationPackageId" Cache="yes" Visible="no"/>
</Chain>
</Bundle>
</Wix>
