There is a different chemical makeup. Take non-pepper fruits, such as lemons, limes, oranges, and grapefruits. These four are all citrus fruits and they all share certain chemicals that make them citrus instead of another type of fruit. Their overall construction is fairly identical - segmented, pulpy flesh with a rind/skin. Their seeds are similarly-shaped. But there are one or more chemical differences that make each unique from the other. In fact, it is the chemical that makes oranges uniquely different from the others that I have become allergic to, while I am not allergic to lemons, limes, or grapefruit. You know that the chemical differences/DNA for these citrus fruits makes them different colors, makes them sweet or sour, makes them smaller or larger than the others, and definitely gives them different flavors. You know also that you can cross these four citrus fruits to result in something different from each of the originals.
Same for chile peppers, but add heat as a component difference. But also note that when considering the opinions of others that a) they are generally true for them but there may be exceptions and b) everyone tastes things differently. I personally, in general, find reds to be more flavorful than other colors, and include chocolates in the "red" category, in terms of flavor. (Plus, many chocolates aren't really ripe until they obtain a tint of red within the brown.) However, I absolutely love the flavor of yellow fataliis. That battery-acid taste that D3monic says he gets from chocolates? I tend to get it from some (but not all) chinenses, most definitely from habaneros, and don't know if he's tried chocolates that aren't chinenses. I definitely do not get it from the non-chinense chocolates that I've tried, such as baccatum chocolates. Fruity? I perceive baccatums, in general, to be more fruity than other types. You can see that you're likely to get a million different answers when it comes to taste perception.
