You can invoke a view controller using an identifier instead of a unique identifier. Take a look a the method instantiateViewControllerWithIdentifier:
That enables you to create view controllers that "float" in your storyboard, without having segue links cluttering up the storyboard.
Once you've instantiated the view controller, you can then present it modally with presentViewController:animated:completion, push it onto a navigation controller, or whatever.
You can even instantiate a view controller with instantiateViewControllerWithIdentifier, then create your own segue object using initWithIdentifier:source:destination, and invoke that segue if you want to.