I know bell peppers aren't finished but when they are fully implemented, I'm suggesting two different methods of obtaining "hotter" peppers from them.
Method 1: When harvesting from a bell pepper plant, there is a very small chance of a Jalapeño seed dropping instead of a bell pepper seed. When harvesting from a Jalapeño plant, there is a chance of a Habanero seed dropping, etc.
Method 2: Bell pepper seeds have a small chance of developing into a Jalapeño plant that produces Jalapeños. Same getting Habaneros to grow from Jalapeño seeds.
Regardless of the method, the idea is to simulate how civilizations have developed peppers to be hotter and hotter.