On the subject of unit lines...these two were done by Kal-el awile back:
One for the Northern Natives, an excellilent example a few things could be changed though. A sword is more advanced than a club for example, plus the Brave is the Iroquois UU currently. We have to sort which units are UUs and which are shared by other tribes in the area. Also, the Horsemen are a special case, which I shall cover below. Also, this was made awile ago, so its missing Utahjazz's Native Musketman(Which I affectionately call the Boomstickman), as well as both his Native Rifleman and Western Native Rifleman. Then again, Kal-el rarely goes into the Musketman replacements in his charts.
One for the Incans:
I'd leave the scouts as they are normally here however. I'd also use some of the the Tupi units. Lets not forget that our mod goes back further than the epic game. For the non-Incan S.American tribes, the would build something else than the Inti Warrior, and the Javelin Thrower is one of the Mayan's UUs. I have some ideas:
Latin Native Archer Line:
Slingers would be the standard first generation Archer unit, except for the Tupi and anyone else you have in mind Civ. These would upgrade to Plumed Archers(AoK graphics) with Archery(Except for the Mayans, who build Javelin Throwers instead), the Plumed Archers upgrade again to Coytl Archers(possible name), theres a few possible graphics we can use for this from Steph's American Conquest collections. The Coytl Archers could then upgrade to the Latin Native Shooters(Again, from Steph's collection), except for the Tupi, who have their own Musketman which could serve as a good UU instead of the Horseman unit, and the Azteks and Mayans, who have the Tlecuatyl.
Latin Native Warrior Line:
The Warrior Line would start with the Tupi Warrior for all the tribes, except for the Azteks, who build Jagaur Warriors instead. That would then upgrade to the Aztek AoK Jaguar Warrior(for the Azteks), the Inti Warrior(Kinboat's) for the Incans, and the Ak Quy for the Mayans and for everyone else? That would then upgrade to the Macan(from Stephs) for the Azteks and Mayans, the Utahjazz Inti Warrior, and what else?
Latin Native Spearman Line:
The Tupi Spearman(by Dease) is good for all the Meso and South American natives. That would then upgrade to the Eagle Warrior(Kinboat's) for the Azteks and Mayans, and Steph's Mayan Pikeman for everyone else. The Pikemen would all upgrade to Musketmen of one sort or another.
Latin Native Musket Line:
The Archer and Spearman lines would converge into the Musketman unit. For the Incans, Maphuche, Jes, Arawak, and Caribs, this would be some sort of Native Shooter, for the Azteks and Mayans, it would be the Tlecuityl. The Warrior line would then converge with the Musket Line at this point, and all of the non-horse offensive/defensive units would upgrade to the Napolianic Era Rifleman units(Grenadier for short), For the Azteks and Mayans, this would be represented by Dom Pedro II's upcoming Aztek Rifleman. For the South American Natives, this could be the Tupi Rifleman. All of those units then upgrade to the standard Civ3 Rifleman, except for the Maphuche, who get their UU.
The Horse Lines(For everyone, Native or otherwise):
In short, there are three kinds of Horse-Mounted units. Spear, Sword, and Archer.
Horsemen, Knights, and Lancers are in the Spear Catagory.
Hussars and Cuirassiers are in the Sword Catagory, as are the mounted clubman(melee)
Mounted Warriors are the the Archer catagory.
The Horse-Mounted Archers were later replaced by Gun welding Cavalry historically, so in game Mounted Archer type units could upgrade to Cavarly type units.
During the 17th, 18th and 19th centurys Cavalry had more diversity than infantry!
Of coarse, during the later eras a big change would occur
The Gun-Cavalry units would upgrade to Bebro's Modern Cavalry, while the Lance Cavalry would upgrade to Early Tanks, and the Sword Cavalry could upgrade to Armored Cars(Which later upgrade to the Mech Infantry)