Only if they discontinued the 3.6. Don't hold your breath. They invested lots of money in the Gen 2. I'd give it 4 or 5 years before it is retired. By then, the 2.0 may be replaced, too. By hybrid or all electric.
The current manual tranny was designed for weaksauce engines.
If the many rumors about the Bronco getting a 7-speed manual tranny it will share with Mustang are true, Jeep will need to up its game. Getrag's/Ford's will handle the 2.3L, 2.7L or 3.0L EcoBoosts as well as the 5.0L V8 (MT88 was spec'ed for 405lbft).