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Although the US captured over half of Mexico, including the capital of Mexico City, Polk did not annex all conquered Mexican territory because:
The American public did not want to bring in large numbers of "inferior" Catholic, non-English speakers as citizens.
His focus shifted quickly to the Oregon Territory issue.
He was afraid it would anger England and France and possibly lead to a war.
He was afraid it might scare other Latin American countries that they too might be attacked and taken over.
He was afraid of adding more territory that might be open to slavery.