I vote for the 1.6 manual. No surprise as that is the one I own. I have yet to see a review where the 1.6 didn't come out on top as the most fun to drive in spite of less power than the 2.0.
I wouldn't worry about resale. The most I've ever lost selling a manual compared to an auto is about $1000. Well worth the price. In fact, one car I had sold for more than an equivalent auto would have gone for. I wouldn't be surprised if that would also hold true for the Fusion. Since it is so rare, people may seek them out.
I don't think parts availability in the future is going to be a problem. Even though it looks like the engine may have a short run, they've made a lot of them. I seem to remember reading that the same manual transmission is used in the Focus and other makes including Mini. Plus, other than a slight chance on needing a new clutch at some point, it is unlikely you'll ever need to do any manual transmission repairs.
The mileage difference may be larger that EPA numbers indicate. It seems everyone with a manual is happy with their mileage, but a lot of 2.0 owners complain.
If you can't get over the power difference, you could consider other cars with more power and a manual. Maybe a new or used Regal, ATS, or CTS?