In your directive 'notificationitem' you have the following code, keep it in mind as i explan:
// if all variables are mapped in this way than works
//$scope.enabled = $scope.subscription.enabled;
The reason why all of the 'isolated' scopes are updating is because of this code in your scope declaration in the same directive (notificationitem):
scope: {
subscription: '=',
index: '@'
},
The equal sign on subscription is angular's way of saying "Whenever the current scope updates, go to the parent and update that value as well." This means whenever you update your 'isolated' scope, it updates the parent scope as well. Since all of these isolated scopes are binding to the parent, they will change as well.
Since you want the subscription.value to be the default value of that text field, you will need to do exactly what your commented code is doing:
scope.value = scope.subscription.value;
This will create an isolated value inside of the isolated scope. When scope.value changes, scope.subscription.value will not. All of the text fields now have their own 'value' to keep track of.
Check out this article for information on directive bindings: http://www.ng-newsletter.com/posts/directives.html
Also, another way to get the default value would be to inject your service into the directive, if you don't like the above solution. Hope this all helps.