The increase in the 'hybrid mode' fuel consumption was the final straw.
Part of the 47 MPG fiasco was that Ford used an EPA loophole to use the FFH test results for the C-Max Hybrid window sticker, since the FFH was expected to sell better. For the Energi vehicles they used the C-Max Energi test results for the Fusion Energi window sticker since the C-Max Energi was expected to sell better (the 2013 Fusion Energi originally cost $40k+). Ford never changed that procedure, even when reevaluating the MPG results. Thus, to see the comparable difference in MPG of Energi versus hybrid you need to compare C-Max Hybrid versus C-Max Energi.
C-Max Energi & Fusion Energi
The Energi powertrain reduces highway MPG in the C-Max by 1 MPG. I'd expect similar results in the Fusion Energi if tested separately, something like 42/40/41. We have always seen better highway MPG in our Energi than we ever got with the FFH because of the larger battery pack. While the impact is small when doing 600+ miles per day with only one charge, it can be felt.