The territory of the Mexican cession was basically chosen because it had the fewest Mexicans in it. This was pretty much straightforwardly racist, as you can see from John C. Calhoun's speech on the subject: http://teachingamericanhistory.org/library/document/conquest-of-mexico/

"Are you, any of you, willing that your States should be governed by these twenty-odd Mexican States, with a population of about only one million of your blood, and two or three millions of mixed blood, better informed, all the rest pure Indians, a mixed blood equally ignorant and unfit for liberty, impure races, not as good as Cherokees or Choctaws?"

As it was, the territories contained some 80,000 Mexicans, who were granted citizenship and theoretical equal protection, but it didn't really work out that way: http://www.pbs.org/kpbs/theborder/history/timeline/6.html