I know how it works. The Congress that we get reflects the gerrymandering of Congressional districts that has been done state by state. The average of people elected to Congress is not biased Republican because voters in Vermont and West Virginia are not balancing out, but because states like Florida and Ohio have districts drawn such that each district is clearly one side or another, with the number of Republican districts significantly exceeding their popular support across the state.
The national result of those gerrymanders is to give Republicans a non-representative edge, and to give the extremists of both parties a much bigger impact than they would otherwise have. And this is not just "how it has always been". This is a trend that is intensifying over time. That is, Congress does not represent the people very well, and represents us less well now than it did a generation ago.
PS You picked a poor example. The only court case in which the third amendment was at direct issue is http://en.wikipedia.org/wiki/Engblom_v._Carey in which it was found that the law was so obscure that bureaucrats could not be faulted for having violated it. Any future violation can also be defended on the same grounds, so it is effectively null and void.