The Wargs of The Hobbit might have seemed more intelligent because Tolkien wrote it as a children's book and might have been more self-indulgent then he was when he wrote The Lord of the Rings. The Hobbit was more of a fairy story--or, at least, what Tolkien thought a fairy story ought to be.
EDIT: Also, the wolves that attacked the Fellowship in Eregion might have been of a different nature than the Wargs that were encountered near Goblin-town. The bodies of the wolves slain by the Fellowship were gone the following morning, suggesting that they were not typical Wargs. Werewolves maybe?