https://www.quora.com/Why-didnt-the-US-also-take-Baja-California-during-the-Mexican-American-War

Although the ports in the peninsula were occupied as many other harbours in the Pacific coast, keeping Baja for the U. S. wasn’t on the original instructions with which Nicholas Trist, the american delegate that negotiated the peace treaty, travelled to México. Once there, he was pressured either to demand more territory, on the view that the victorious invasion exceeded the expectations of American military and politics, or to abandon the talks and return to Washington so that the annexation of México to the States would become a fait-accompli.

However, Trist not only resisted the pressure from James K. Polk but he even persuaded the mexican delegates to hurry up with the signing, since there was a growing movement in the United States to directly annexate México or demand the occupied mexican states of Chihuahua, Nuevo León and Baja. Trist convinced the mexican diplomats to cede “only” the northernmost states in order to keep the other occupied regions, and ultimately the nation. Under the Guadalupe-Hidalgo treaty, the western border between México and the U. S. would run from the convergence of the Gila and Colorado rivers in a straight line to the Pacific Ocean, one mile south of San Diego, in the estimated limit between Alta and Baja California.

Thus, thanks to Trist, México kept the strategic although almost deserted peninsula.

(http://www.autoadmit.com/thread.php?thread_id=4030340&forum_id=2#36460342)