An alternative troop tree is realistic for the Americans and in theory also for Mexicans if the roles were reversed. But if the domination is in the case of a player being an indian or bandit/outlaw, then it is probably better for those of both indian and bandit/outlaw culture to remain mononational (when conquering an opposing city, you continue recruiting your own kind) and in this case, have a unique troop tree
only for
Mexican and
American occupation of
Native-American or
each-others lands. These soldiers would be based on an "integrated" population which cannot achieve the professional heights as the homeland armies but be effective nevertheless.
Though one could use a little fantasy and imagine what an origionaly American ocupied town would be like when occupied by Indians. In my opinion the Indians would most likely slaughter everyone and burn it to the ground. Then put tents over the ashes, but thats just my opinion

. In fantasy for the sake of gameplay, I could imagine the Indians to make use of the guns they would find there and perhaps in this scenario, one could recruit a more modern Indian warror type which would be worse than your origional Indian warriors like I suggested for Americans and Mexicans. But for simplicity and realism, I would vouch for leaving Native-American and bandit/Outlaw factions with a mononational recruiting system and reserve the unique troop trees for Mexican and American domination.
Perhaps I should have put this in the suggestion thread

.
Edit: To have an Outlaw/Bandit culture on towns conquered by Native-Americans like DamienZharkoff suggested, could also make for a potential alternative.