I had a similar need and had the same problem accessing the scope using angular.element. I was was able to solve it as follows though:
In your main/parent controller do something like this:
$scope.food = 'Mac & Cheese';
window.$windowScope = $scope;
$window.open('views/anotherWindow.html', '_blank','menubar=yes,toolbar=yes,location=yes,resizable=yes,scrollbars=yes,status=yes,personalbar=yes');
Then in the child window controller you can access $windowScope like this:
$scope.parentWindow = window.opener.$windowScope;
console.log($scope.parentWindow.food);
An alternative to putting data directly into the scope would be to use $window scope to broadcast and/or emit events, which is the preferred way of cross-controller communication in angular.