Could this be All Tomorrows by C. M. Koseman? It was published online (only) in 2006. From the Wiki entry: "Following the colonization of Mars, a brief but catastrophic civil war takes place between Mars and Earth. ... Humans then encounter a malevolent and superior alien race called the Qu. The Qu's religion motivates them to remake the universe through genetic engineering [and they] bioengineer the surviving humans as punishment into a range of exotic forms, many of them unintelligent".