In SharePoint 2010 service applications, the managed metadata service connection properties can be set using the cmdlet Get-SPMetadataServiceApplicationProxy

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# Get Metadata service application proxy 
$metadataserviceapplicationname = "Managed Metadata Service"
$metadataserviceapplicationproxy = get-spmetadataserviceapplicationproxy $metadataserviceapplicationname

# This service application is the default storage location for Keywords.
$metadataserviceapplicationproxy.Properties["IsDefaultKeywordTaxonomy"] = $true

# This service application is the default storage location for column specific term sets.
$metadataserviceapplicationproxy.Properties["IsDefaultSiteCollectionTaxonomy"] = $true

# Consumes content types from the Content Type Gallery
$metadataserviceapplicationproxy.Properties["IsNPContentTypeSyndicationEnabled"] = $false

# Push-down Content Type Publishing updates from the Content Type Gallery
# to sub-sites and lists using the content type.
$metadataserviceapplicationproxy.Properties["IsContentTypePushdownEnabled"] = $true

$metadataserviceapplicationproxy.Update()