App Pool advanced settings using Powershell Desired Configuration State

Yes, a custom DSC resource is the only way to do this with DSC. If you are able to use PowerShell scripting without DSC, you can use the WebAdministration module module to create the pool, and then modify it from there.

$appPoolName = "MyAppPool"
New-WebAppPool -Name $appPoolName
$appPool = Get-Item "IIS:\AppPools\$appPoolName"
$appPool.processModel.identityType = 3
$appPool.processModel.username = "someUser"
$appPool.processModel.password = "somePassword"
$appPool.managedRuntimeVersion = "v4.0"
$appPool.managedPipeLineMode = "Integrated"

Update 1/31/2015

In the PowerShell.org community DSC modules, someone made a cWebAdministration pull request that apparently includes "37 app pool config options". Might be a great solution.