Control of both houses of Congress and the White House has swung back-and-forth for the past 30 or so years - ever since Reagan's run came to an end, the last truly dominant President we've had. (Obama won handy victories in '08 and '12, decisive victories but nothing like the Reagan '84 map - and Obama couldn't keep control of Congress for Democrats.)
So, historically speaking, this is one of the longest periods of time America has gone through without one party being the "naturally in charge" party.
It would seem therefore that the electorate is hopelessly confused and divided. That's undoubtedly true to an extent. But there's another story here, which is that the last 30 years would actually be a "Democrats-naturally-in-charge" period of our history if election results actually matched the popular vote.
But because Republican support has consolidated in small/rural states where voters' votes (esp. for Senate and in the Electoral College) count more, even as Republican share of the vote has gone down, Republicans have remained competitive.