Question phrased in such a way that I am not sure what you want to do.
Create a New Pepper - Easy, start with black / brown varieties, cross away, see what you get, and then years of selective seed saving and you might have a stable new pepper. CPI has a fantastic guide to crossing chili peppers.
Change Color of Existing / Established Pepper - My opinion is can't be done because I feel that once you cross two peppers, the offspring are no longer the original pepper.
Let Nature Take its Course - What Kraken said about natural varients I believe very much. I have chocolate reaper growing. First year had a single plant, saved seeds, horrible germination rate. Next year, grew true to mama plant. Saved seeds. Kind of thinking the germination rate improves with time due to auto culling.
Long story - Birds do not fully digest pepper seeds. Bright colors attract birds. So chances are natural selection would cause brightly colored peppers to expand their domain much more than chocolate / black peppers. Thing is, mother nature doesn't tend to throw away dna. Instead, the genes that failed wind up in the mix somewhere but recessive.
Now this is real sixth grade earth science, fruit fly, eye color stuff. It is much, much, much more complicated. But this is the basics of what I think is going on. I -think- the darker colors are recessive but generally in there. When two peppers of the same variety cross pollinate, if both have the recessive gene for brown then some of their offspring will have only that recessive gene for color.
BR = Brown Gene (recessive)
RD = Red Gene (dominant)
Parent A is Red but has both genes - BR n RD
Parent B is Red but has both genes - BR n RD
Offspring Could be:
BR n RD - Will be Red cause is dominant.
RD n RD - Will be Red cause that is all that is in there.
BR n BR - Will be brown because that is all that is in there.
Where a monkey wrench is thrown into my thinking is that peppers tend to self pollinate. That being the case, I would imagine lots of folk should have noticed chocolate reapers. I have only red about three people thus far. Two in the US and on one in the UK. The one in the US sold his seed stock right off the bat, so I imagine we will hear more about it soon. Then again, there was the horrible germination rate that I observed, so maybe not till it is grown out a bit.
In closing, take note of the whole thing on how this comes from sixth grade earth science. I am no expert and constantly humbled by mother nature's roulette wheel. Got two health, bright, intelligent kids. No clue how that happened.