How to thicken Chili without compromising flavor
As noted above, reducing the liquid through evaporation will thicken up the chili but you run the risk of burning/scorching the bottom and it can take a long time at lower temperatures. What I like to do is to take some of the beans (I prefer black beans in mine) and mash them up into a thick paste and then stir that into the chili. The starches from the beans will help thicken up the chili and you aren't adding anything that isn't already there. I have also seen people do similar things with cornbread.