There are a lot of mechanisms that prevent the will of the people from being expressed at the federal level right now, but the two-party system, first past the post, and Citizens United are probably the big three.
The increasing power of the executive and the courts have come about almost entirely because the legislature has abdicated its power and responsibility. One of our two political parties is heavily invested in preventing action at the federal level, and the other two branches have stepped in to fill that power vacuum. This is sort of necessary, in that it keeps our country from grinding to a halt, but it also consolidates power to fewer, and in many cases unaccountable, people.
There are, unfortunately, no easy solutions here.