I’ve driven both the AT and MT FR-S, I ended up buying the MT.
The auto is pretty quick and it eliminates all of the hassle of driving in traffic. You still get the awesome chassis and steering feel of the 86. It’s not dual clutch precise, but it’s not CVT bad. For me personally, the cars I’ve owned with a “sportier” auto (like the DSG in my GTI) I rarely used the paddle shifters. It’s too video game feeling to me.
A manual will always win for the connection you have to the car, and you can ALWAYS make sure you are in the right gear, because you get to select it. The MT in the 86 feels so amazing when the gearbox is happy and warmed up. This is always a car that likes to be hustled, it never feels very happy chugging along slowly. My one warning to anyone buying a manual 86, it’s not a transmission that you can just slam into gears. It’s similar to cars like the S2000 and WRX/STI. It likes precise shifts, and the synchros for 2nd gear especially are temperamental. That being said, when you nail several shifts in a row you feel like a driving master.
My choice would always be the MT, unless you have to drive in a lot of heavy traffic. In that case get the AT, or buy an 86 as a weekend car with a manual. I don’t think someone is any less of a driving enthusiast if they choose the auto 86. It’s a blast to drive with both transmissions.
Personally, I'm going MT. I've been driving a friend's car to get use to MT again, and my AT car feels so boring now. At the same time, I'm not getting rid of it because it will be a good everyday/long trips kinda car.