var x = [[1, 2],[3, 4],[5, 6]];
var y = [];
var temp = [];
var i = 0;

while ( i < x[0].length) {
  var c = 0;
  while ( c < x.length ) {
    y[c] = x[c][i] ;
    c++

  }
  //console.log(y);
  temp.push(y);
  i++
}

console.log(temp);