That's because their chief weapon is fear and surprise. Their
two main weapons are fear, surprise, and...
On topic, are you talking about the mineral composition or the basic shape of Central America? If it's the latter, that ain't gonna help you much since you can't really do a whole lot with the worldgenerator right now.
Here's some simple advice: Add the [CAN_STONE] tag to spears, axes, picks (if you want anyone besides the Incas to mine), and arrows. Or anything else you might want made out of obsidian (note: also requires a piece of wood).
I don't think it's currently possible to make cloth armor, but you can always give it a shot. Clothing and armor are in the same spot in the raws, so you can just find the tag that allows something to be made out of cloth (I think it's [SOFT] or something) and slap it on some armor type.
You might also want to add "Atlatl"s. Spear-slings. Just create and "atl" weapon, make it use crossbow skill (unless you want a non-playable race to have it, then you can put whatever you want. It's just that crossbow is the only one you can select for your military), and create a new ammo type called an "Atl dart". These things are essentially javelins with a launcher, so they'll do a hefty amount of damage.
Oh, you can also add the [WOOD] tag to some weapons so you can make it out of wood. Spears and maces seem reasonable enough.
Native gold nuggets provide the same value modifier as smelted gold bars. A craft made out of gold stone is worth the same as a craft made out of gold metal, however gold stone can potentially be snapped up for other meaningless uses and can only be used if it's turned on in the economic stones list.
You might want to consider adding "Maize" as a crop type, edible raw and brewable into Maize beer. I'd also say add cacao/cocoa, but there's no real way of doing that except for making it booze. Schnapps, anyone?
Add some Quetzal bird-vermin while you're at it, and make them rather high-value pets (not that you'll ever catch one, mind you...). There's also some type of wild jungle-boar that's a good food source, but I can't really remember the name offhand (peccaryn?). Don't forget to add some fantasy critters from their mythology.