Tematlatl?

[amagi]

Also the Spanish might be split into Cuban and Vera Cruz factions, that might help with balance.

The Mesoamerican spearmen have no armour but are given stats for armour.

Too many factions have the Sun God religion. The Aztecs were notoriously hated because they worshipped the war god and kept their region in conflict.

Perhaps more could be done with the sacrifice unit cost/upkeep concept?

[Myth]

All of these can be modded in the game. If you are willing to put in the time to do it, you can do it yourself and we can even host your mod/overhaul project here! FYI I like your suggestions. Also add to this - the natives need some sea transports to be able to get to the Spanish islands. They should be weak for naval fighting but fit enough to transport troops.

Also the Apache warpath (aka. the Jihad mechanic) is IMO overpowered considering that nobody else has it.