I'd go to the store and ask if you can upgrade to the CE. If they say they can't do that I'd ask about moving your deposit over to Arkham City, and then pre-ordering the CE elsewhere.
This sounds like your pefect option. Get Arkham City from the store and you still supporting them, and get the CE elsewhere since you want that as well.
Now why would you want the CE? I would say buy both games from the store since both of them will cost the same as the CE.

I would rather get Skyrim and the strategy guide wich I will have more use than what is in the CE.