well i own both a 2007 4runner and 2010 VW TDI.
my opinion would be that i would take the TDI any day over my 4runner. plus the airbag setup in the VW is amazing offroad and along with the differential settings on it make it possible to go just about anywhere. another plus would be the closer wheel base.
i would take my 4runner if i knew something would happen because everyone knows German parts are crazy, price wise.
although i wish i would have bought the 2008 v10 4.6 TDI rather than the v6 3.0 TDI just because of the power difference.
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Fuel wise for the VW i try to only buy from shell, it is the best fuel stations anywhere in my opinion, for diesel or gas.