Finally had a chance to check out the new Spy Museum and it was incredible though somewhat overwhelming. We left after about 3 hours because it was getting late and we were hungry.
I'd recommend trying to get there around 10 AM, then spend until about noon, then either hit the food court behind it or walk to the Wharf for lunch, and then go back. It would provide a nice break and more time to see and do everything inside. The Wharf is about a five minute walk. We went there for dinner afterwards.