I've always been a fan of manual trannys....until I started having to deal with rush hour traffic on a daily basis. I truly think I started walking with a limp because my left leg muscles were developed more than my right....
Seriously, I think manuals are fading away for several reasons. Automatics can give higher MPG's because the onboard computer can shift when optimal. Makes the manufacturer look better on paper. Also, not many people CAN drive a stick anymore. It's going the way of the blacksmith. When people find out that you can drive a stick, they actually respond with, "Really ?!?", like it's something anachronistic, which, in a sense, it is. I'm waiting for a millennial to slowly stroke my arm and say, "Aww, you so old..".
For a weekend/off-road driver or a true Jeep (I'm talking M-series, CJ's, Wranglers and such), a stick and a REAL transfer case is the only way to go. For a daily grind commute, yeah, I'll admit it, I'll take an automatic.
Unfortunately, most Jeeps sold today are for just that; daily commutes. Off-road today means turning off the road into your driveway.
As far as increasing value, the market for manuals is obviously already low or they'd still be pushing them. So the market won't increase once they stop, it'll actually get even lower because the market doesn't want them. Buyers will be looking for automatics because they've never learned on a manual. It's all economics. I'm making up numbers here, but let's say out of every 100 Jeeps sold, 5 or 10 have manual trannys. It's not worth the cost to continue to satisfy such a small market. A walk through a dealer lot can verify this. Way more autos than manuals. Because that's what sells.
I compare it to crank starts. At one time you had to manually crank start your engine. Then the electric starter came out. Gone were the cranks. If buying a car, would you choose the old crank start or the new easier electric start ? Automatic transmissions are plain easier.
Yes, manuals are much better...for certain situations and reasons. But not for the average schmuck behind the wheel. So manuals are going bye-bye.