I've had both - the 3.6L is vastly superior to the 4.0 in every single way. It's not even close, and I had arguably the best iteration of the 4.0, the port injected TJ version. It was a great motor but ~100hp less than the 3.6 and 25% less efficient with no perceivable benefits.
As to the reason manuals are going away - they're objectively worse than autos in almost every way now. Worse fuel mileage, worse towing, worse acceleration, worse off-road. Even up to 5 years ago that wasn't the case, but if you get a manual Gladiator you give up 2500lbs in towing and get worse performance. I was a manual die hard, even going so far as to go through the pain of converting a couple of cars from auto to manual, but in the last 5-10 years autos almost universally have surpassed manuals in performance and the new JL and JT were the first vehicles I didn't even consider the manual. I still enjoy rowing my own, but I have a couple of "antique" sports cars for that, which, much like carburetors, are where they belong these days.
I agree with this. I have owned over 20 jeeps in my life and have had most of the engines, mostly with manuals. My current 19 JLR is easily the best of the bunch.
I still got the 6 speed manual with the 3.6. LOVE IT! This was Not my first 3.6 either. I have one in a Durango.