The AI for the Natives is spawning Braves at a very high rate. Too high in this current version 1.1 imho. The map is literally crawling with braves and when they are raiding in the early 1600's they come with just not 1 or 2 braves units but up to a 6+ at a time. And this is just on Explorer level.
There are also too many Native cities.
That's something present in vanilla too, it's strange you are the only one who has noticed this too.
I thought about this some time ago and I reach to the conclusion that the main problem is how native units are generated.
First we have units and then professions. The native unit has no cost in food or any other yield, so all cities are constantly creating new native units. Note Europeans can not do that, the city grows and a new unit appears.
Native use the opposite system, they grow and they can create population by using production!
Ray could do whatever he wants; but here are my experiences about what I did with this problem. Also note is still something being tested so I'm open to other things.
I added a yield requirement to the native unit. Food, 50. That way I wanted to relate in some way the amount of units a city can support with the food availability of that city.
First impression: it works as intended! Natives start with a standard number of units, but now the have to spend more time and resources to create new units. Also due to this system, they now use more population to obtain food; but note that at any moment they can convert population in brave units so there is no bad side of this. Only the grow rate has changed.
I also thought about changing the profession... why they can create braves without any type of weapon/yield requirement? So I tried also with food. The results are mixed; it adds much more playability to the game since now you can capture native cities (or better said, the population units which have not been converted into braves). So conquering native cities really makes sense and it's not like they can convert anything into soldiers.
But it requires a small adjustment to 1 AI function; because the AI always try to convert native units to brave by default (it's the default profession for that unit) so it will produce several asserts during game. There is no more game problems associated.
Finally I added other thing, I created a new profession similar to the actual brave. The idea is to let the AI convert native units into braves as default but that brave unit has some tweaks in strength or other parameters (can be used along some limitation as the default one). And then the new profession would have the same stats than the actual braves, but they would required food.
This way you reduce the real spawning rate of soldier units while you allow natives to still convert without costs population units into some type of weak unit.