If the polygons are not aligned then they have to be aligned. I would do this by finding the centre of the polygon (average in X, average in Y) then incrementally rotating the polygon by matrix transformation, project the points to one of the axes and use the angle of minimum stdev to align the shapes (you could also use principal components). For finding the intersection, a simple algorithm would be define a grid of points. For each point maintain a count of points inside one polygon, or the other polygon or both (union) (there are simple & fast algorithms for this eg. http://wiki.unity3d.com/index.php?title=PolyContainsPoint). Count the points polygon1 & polygon2, divide by the amount of points in polygon1 or Polygon2 and you have a rough (depending on the grid sampling) estimate of proportion of polygons overlap. The intersection area would be given by the points corresponding to an AND operation.
eg.
function get_polygon_intersection($arr, $user_array)
{
$maxx = -999; // choose sensible limits for your application
$maxy = -999;
$minx = 999;
$miny = 999;
$intersection_count = 0;
$not_intersected = 0;
$sampling = 20;
// find min, max values of polygon (min/max variables passed as reference)
get_array_extent($arr, $maxx, $maxy, $minx, $miny);
get_array_extent($user_array, $maxx, $maxy, $minx, $miny);
$inc_x = $maxx-$minx/$sampling;
$inc_y = $maxy-$miny/$sampling;
// see if x,y is within poly1 and poly2 and count
for($i=$minx; $i<=$maxx; $i+= $inc_x)
{
for($j=$miny; $j<=$maxy; $j+= $inc_y)
{
$in_arr = pt_in_poly_array($arr, $i, $j);
$in_user_arr = pt_in_poly_array($user_array, $i, $j);
if($in_arr && $in_user_arr)
{
$intersection_count++;
}
else
{
$not_intersected++;
}
}
}
// return score as percentage intersection
return 100.0 * $intersection_count/($not_intersected+$intersection_count);
}