First a correction. In my former post one should have read : jungles should NOT be settling places for cities (still IMHO).
About wild "barbarian" animal units : yes, I think that means you should add them by hand. Another idea is to actually limit their movement in some areas (such as jungles).
El Dorado was far from thriving when I discovered it.
Well, of course, I discovered it early and I raged an attrition war with 1/2 conquistadors when I realized how many archers it got. But it was in mere jungle as well, which is NOT the best area for growth
Maybe you could add the 7 cities of Cebola as treasure units (invisible except for conquistadors ?) that must be brought back to Canaries. Maybe it would be too similar to Conquest : Age of Discovery but I think it would force to go for more scouting and ships would have a meaningful return trip. Besides it would add something else than mere destroying (not because destroying is bad

but because sometimes you get bored waiting for reinforcements

).
About time length : no, I did not realize. I just played slowly because I thought I had the time. And even with that I hardly built any city (2 South of Panama actually).
I don't think you could have made Medieval Infantry out of Indians and I think capturing them with Conquistadors provide high enough a number of them but that is your scenario...
About pedias : well, I was not trying to force you or anything. It is just for scenarios it might be useful for pedias give precious informations about abilities.
About wonders : I am definitely no specialist of the area. But I presume you can use many wonders from Meso-America and Age of Discovery conquests. Sun Temple, Moon Temple, ...
Ah yes, BTW, one "bad" critic : I think it is nice you tried to represent the return of the white god (ie Hannibal

). Your way might be the only way to represent it or the best way but it is personal I just don't like it.