There are a number of issues. Almost certainly, if all of Mexico were annexed by the USA, there would be major questions regarding how the territory would be adnimistered. One thing is sure. Mexicans (whether hispanic or mestizo) would not be segregated or enslaved. They weren't in New Mexico, and California and they wouldn't be if all of Mexico were incorporated. Also, since most Indian peoples in central and southern Mexico were already "pacified" farming village dwellers, I doubt you'd see the forced relocations and reservation system for American Indians used in Mexico. The treatment of Mexicans of african descent might be problematic, and would be a major controversy in the US congress. My gut feeling is that some compromise would be reached that did not re-enslave people aho had been free Mexican citizens before annexation.
One question is how Mexico would be administered,subdivided and territories for eventual US statehood established. Would existing Mexican states be retained as territories or new internal boundaries established? Regardless, there would be a major influx of Anglos into Mexico, and I tend to believe (as in New Mexico and Arizona) former Mexican territories would only become viable candidates for statehood when an Anglo majority was reached. This may never occur in densely populated central Mexico itself, which raises the possibility not all of Mexico would be fully incorporated in the US federal system. Parts of former Mexico might be placed on a track similar to Puerto Rico - one in which independence is a possibility.