Am I allowed to have the command call the view for an example with TweenLite.delayedCall()?
for sure command shouldn't call the view but just send notification. Observer will respond with view right action inside the view. TweenLite can be used - that is not a problem even with delayedCall however I do believe that all transition functionality should be stored within the View. Mediators react for received notifications that can carry a object contains transition sequence. That is my solution.
If you want to take them down one by one... hmm....
you might create a function that will be called everytime one of them has been removed or tweened. You can fire it using
TweenLite.delayedCall(delay:Number, onComplete:Function, onCompleteParams:Array):TweenLite
Function will check if there any objects left - all available in the conatainer or within array that can store it. If yes will take another from the stage or list you predefined and perform expected action. My feeling is to keep it simple but not too much.