Lot's interesting, and repeated viewpoints in this thread. Of course, this is an enthusiasts' forum. We like cars, so we have opinions, and a higher number of MT folks here than the North American population per capita, I'd wager.
To the OP:
1. once you actually really *learn* a stick and live with it for a while, 3 pedals is a no-brainer-- you don't even notice.
2. on technical terrain, mountain roads, slippery surfaces, steep up/down grades, the manual will very humbly let you know you have much more control via engine braking, or less wheel-spin runaway if the traction drops during acceleration.
3. growing up in the snow, manuals literally double the amount of driver control, regardless of plunking the shifter into L.
Some are more fun than others. Short-throw smooth shifter, like a miata or some civics, Yea! My older subaru legacy-- kinda notchy and slow... I had to learn to make it sing, but was also very good for clutchless shifting. Long stick on older F150-- I LOVED. Notchy 2nd gen miata, fun but a little harder clutchless.
If you REALLY want to drive the car, especially an underpowered car surrounded by jags, benzes, and M3's, heel-toe shifting through city traffic made a commute entertaining.
Yes, cycling injuries made the left knee a bit more aggravated with extended stop-n-go. Finally, a wrist injury pretty much made me kiss a MT goodbye. But from time-to-time, I'll jump back in one. It's like riding a bike. a minute to learn the clutch, and then it's FUN!!
AFA off-roading--- AT vs MT is a huge driver preference issue. Low range takes a huge stress of the clutch. 3 pedals requires more coordination. MT offers better descent control.
AFA sports driving, the right gear, and that MT allows you to quickly induce more or less steering by shifting the "weight" between front and rear. This can be kinda/sorta done in an auto, but not with precision or quick transitions.
So, as a full-time auto trans driver now... if someone told me I needed to make a technical drive through snow, racecourse, mud, or any other control-oriented path, and wrist pain wasn't an issue, I'd take a MT hands-down.
P.S.-- my brother travels the world as an ice climber and river rafter. It's his full-time gig. Due to longevity and parts sourcing, manuals are the norm in most other countries.
M