The current version of Time Capsule is the 'new' one. It was released a few months ago. So, the one on the Apple store is the one you want.
Typically, when Apple updates a product they remove the old inventory, so, if you are purchasing from your local store you will most likely get the new one. However, it's always best to check.
One of the features in the new TimeCapsule that could identify it would be the guest network feature that allows you to setup a separate network for guests that doesn't allow access to your private network. This feature is not in the older product.