I think the assumption that you're making -- that evolution has a point, and that some structures will provide advantage no matter what-- may be dangerous. Evolution has no point, and no motive--it just happens. Sometimes I think 'natural selection' is a misleading term for the simple phenomenon of some things living and reproducing, and others not. In some instances, there may not be any advantage of some genes over others--it may just be the luck of the draw. Such would be the case with some founder effects or bottlenecking events, as someone mentioned.
Natural selection, where adaptive variation persists over deleterious variation, is certainly a mechanism of evolution--but not the only mechanism. To suggest that it is the only mechanism, and that it is determinant, only lends credence to the ID argument, and undercuts the subtlety and complexity of the process.
As Stephen Jay Gould said, if we were to replay the tape of life, I'm sure things would come out differently. If evolution were determinant, that would not be the case.