PS + CSOM to iterate webs/lists and set a property..

IterateWebsAndListsEnableVersioning.ps1

. .\TopOfScript.ps1

$enableVersioning = $true

$rootWeb = $clientContext.Web
$childWebs = $rootWeb.Webs
$clientContext.Load($rootWeb)
$clientContext.Load($childWebs)
$clientContext.ExecuteQuery()

function processWeb($web)
{
    $lists = $web.Lists
    $clientContext.Load($web)
    $clientContext.Load($lists)
    $clientContext.ExecuteQuery()
    Write-Host "Processing web with URL " $web.Url

    foreach ($list in $web.Lists)
    {
        Write-Host "-- " $list.Title

        # leave the "Master Page Gallery" and "Site Pages" lists alone, since these have versioning enabled by default..
        if ($list.Title -ne "Master Page Gallery" -and $list.Title -ne "Site Pages")
        {
            Write-Host "---- Versioning enabled: " $list.EnableVersioning
            $list.EnableVersioning = $enableVersioning
            $list.Update()
            $clientContext.Load($list)
            $clientContext.ExecuteQuery()
            Write-Host "---- Versioning now enabled: " $list.EnableVersioning
        }
    }
}

foreach ($childWeb in $childWebs)
{
    processWeb($childWeb)
}