Believe it or not, there have been several instances of the Motorcraft battery going bad early or right from the start, perhaps you were a victim! But ignoring that for a second, the usual culprits have been loose battery terminals, a bad BCM, transmission sensor, or skipping CD/bad APIM draining power from the battery. They cause a parasitic draw on the battery, which can be established by standard electrical diagnostics.
Do you drive sufficient distances every day to keep the battery charged? Shouldn't go dead in 3 days without that parasitic draw though. If the alternator is not doing its' job, then maybe.