First of all, you have to make a distinction between civs that did not use Metals in their armamaents (Aztecs, Zapotecs, Mayans, Tlaxcaltecs…) and those that did (Incas, Chimu, Tarascans…).
This is important because it completely changes the types of troops a culture could actually field, and what upgrades it would show in the game.
The values I will present are all imaginary, as proof of concept, not to be taken literally.
Stone Weapons
Peoples without Metals should have Weapons and Armour sidegrades, more than upgrades, as this more realistically exemplifies the difference between an Obsidian and a Flint weapon. For Example:
-Flint Blades - Infantry and Archers/Javalineers get a Bleeding passive ability with 10% chance per attack.
-Obsidian Blades - additional +5% Bleeding Cance, +5% increased Attack Speed for Infantry.
-Jade Blades - Infantry Damage ignores 5% Armour, Archers and Javalineers have 30% of Ranged damage converted to Melee.
-Atlatl - Javalineers +2 Range.
-Fletching - Archers +1 Range.
-Braided Slings - Slingers get get an Impact passive ability with 15% chance per attack (slow or stun enemy units).
Cotton Armour
A case for non Metal Armour would be more in line with Eurasian upgrades, but cheaper and weaker, on the later ones:
-Cotton Armour - +10% Melee and Ranged Armour (as normal with Eurasian civs).
-Diamond-Pattern Shirt - +15% Melee Armour.
-Salt Drying - +15% Ranged Armour.
-Jade Gorget - +5% Melee Armour only to Nobles/Priest units.
-Salt Weathered Shieds - 5% Ranged Armour only to units using Shields.
Metal Weapons
Steel being obviously out of the question, still leaves us with a decent amount of Metals to work with. It is important to know that several of the Andean cultures, and the Tarascans, alloyed Copper with other Metals, with produced a softer Bronze than in the Old World, but Bronze is still very hard and resilient, regardless.
They also used Meteoric Iron, left on the surface presumably by fragments of the meteor that killed the Dinossaurs. Iron was much weaker than Bronze, but also much more available, which is one of the main reasons it replaced it in the Old World, centuries beforehand, as Bronze is an alloy of 2 or more Metals, one of them being rare Copper, and the most common other one being Tin, which are not often found together.
The Incas used Arsenic to make Bronze, while the Tarascans used Silver and Gold, for example.
Realistically, such upgrades would be closer to Eurasian upgrades, and could look like:
-Copper Weapons - +10% Damage for Infantry and Archers.
-Meteoric Iron Weapons - +15% Damage for Infantry and Archers.
-Bronze Weapons - +20% Damage for Infantry and Archers.
-Lead Bullets - +5% additional Slinger Impact chance.
-Arsenic Bronze - Infantry, Archers and Javalineers get a Poison passive ability with 10% chance per attack.
Metal Armour
Cultures that had Metal Weapons also had some forms of Metal Armour. Meteoric Iron, however, was not used in this manner, possible because it was both too scarce and maleable at the same time, which made it subpar when compared to Copper.
Therefore, I would suggest the first upgrade to still be Cotton Armour. It would look like:
-Cotton Armour - +10% Melee and Ranged Armour (as normal with Eurasian civs).
-Copper Vest - +15% Melee and Ranged Armour (as normal with Eurasian civs).
-Bronze Vest - +20% Melee and Ranged Armour (as normal with Eurasian civs).
Land Units
This section would also have to be divided between Central and South America, with big differences between the 2.
As an example, in Mesoamerica, Bows and Slings were looked down upon as being simple Peasant Conscript weapons, not worthy of a real Warrior Class, which vastly preffered Javelins as their main Ranged weapon, as combat in the rainforest did not really favour the greater Range of Bows, compared to the brute force of a more weighty Javelin.
In these circumstance, Central American Bowmanship fell way behind what was developed in the Old World, specially Asia, where the Bow was still used all the way till the 19th century in many cases.
In the Andes region, the reverse was true, as Mountain Combat highly favours greater Range, than what Javelins, even with Atlatl arms, could provide.
It is worthy of note that most of the Native cultures people ask for, did not solely rely on stereotypical Spears, Shields and Bows/Javelins. Slings, Swords and Two-handed weapons were common.
The Tarascans and Mayans had Two-handed Axes. the Aztecs had Macuahuitl, the Incas had Halberds, the Chimu had Maces…
There are several unit types that can be explored, but none of them could run as fast as a Horseman either.
The Aztecs had their Jaguar and Eagle Knights, aswell as several lesser orders of Peasants that sought social ascension by way of enlisting in the military. Warrior Priests or Religious Orders were also very common in the Americas. These could provide more elite variants of your normal troops, but still less formidable than Eurasian counterparts.
A similar logic could be applied to unit line upgrades, that would become more like sidegrades, as to both maintain a semblance of realism while still interacting with game mechanics, and providing meaningful progression.
As an example:
-Aztec Tlamani Spearman upgrade into Cuextecatl Spearman, with only a small HP upgrade, and now also trains two units at a time for the same cost.
-Aztec Cuextecatl Spearman upgrade into Papalotl Spearmen, with a small Attack Speed and HP upgrade, and now no longer cost Wood to train.
-Aztec Papalotl Spearman upgrade into Eagle Spearman, with a small Speed upgrade, and now deals bonus Damage against Infantry.
Many similar examples can be had, such sidegrades would ensure that the civs would stand a fighting chance, while also not being dependent on engorged and unrealistic stats blocks, that make no sense for the level of warfare they actually pacticed.
Other sidegrades could be like:
-Trains instantly.
-Resource cost changed or diminished.
-Population cost reduction.
-Trains in bigger batches.
-Trains in tandem with another unit type for support.
-Gains ability to raid for resources.
-Gains bonus Damage against a different unit type.
-Gains Camouflage (stealth while still, outside of defensive building ranges, and not attacking).
-Gains Warcry (triggers like Arkantos in AoM, but to a lesser area and effect).
-Gains Climbing ablity (can get ropes over Walls to climb).
And so on.
Water Units
Sorry fam, but this is impossible without being HIGHLY unrealistic, to the point in which we are going full-on Fantasy.
AoE3 tried, and it just ended up goofy. AoE gameplay is mostly on Land maps anyway, so it will not be a problem if Native American civs suck on Water.
No way should even 100 Canoes or Rafts be able to face 2 Carracks or Junks.
Siege Units
Since the Devs went with the Stronghold approach to Walls, we actually do have a wealth of options.
Sappers that dig under to damage Walls by setting the foundations on fire, Ladders that allow units to climb them, burning sacks of poison herbs or gourds filled with Hornets, Mantlets that absorb Ranged attacks for your units like Rams do in AoE2, simple and cheap Ram Teams, and even Poison Smoke burning in pyres and fanned towards the enemy.
Many of these would not actually destroy Towers or Castles, but they could kill the Archers on the Walls, and simple torch throwing could slowly deal with the more fragile buildings behind them.
General Gameplay
We know that several American Empires had very advanced agriculture, which allowed to have massive population densities that their otherwise less sophisticated tools would allow (try plowing the fields with an Iron Plow, and then with a Wooden Plow, and see how much harder it is, specially without pack beasts).
Combined with their Monumental Archtecture, these civs could be geared towards Economic Boom strategies, that would allow them to get their weaker technologies faster than the Eurasian civs, and greater troop numbers or replenishment, that would leverage their advantages to cover for their disadvantages, in more unique ways.
One of these civs could have very cheap, yet strong, buildings, and also get cheaper troops with Age Ups.
Another could have upgrades that slowly shift unit costs towards Food, while also having one of the best Farming economies in the game.
Even a third case could easily be made for a civ that just gathers map resources faster, and overwhelms earlier, with numbers, propelled by their early Resource Gather bonii.
Ending Argument
Please do comment on my suggestions, and post your own. Keep in mind that the purpose of this thread, is to imagine how a REALISTIC (no Magic, not silly Canoes that deal as much damage with an Arrow as a Cannon, no Jaguar Warriors with more HP and Armour than fully Plated Pikemen, no imaginary units that did not actually exist to fill rosters…) Native American civ lineup would look like, in AoE4, where the main developer straight up said he wants this to teach actual History.