Jelali was definitely involved. He definitely trained Affleck for The Town. The Town's official workout video has Jalali demonstrating Affleck's workout and diet. And Affleck has even endorsed Jalali.
I think Jalali was involved early on, early on he used to tweet a lot about Affleck's training and progress but off late he has stopped, I believe he was fired and these new guys were taken on.
While it is true that in the physical department 300 2 did not live up to the original 300, that's more down to the actors than to the training of Gym Jones which was still world class. The actors as has been implied did not put as much into it, or were not able to put as much into it, as the original cast did. Hence the less impressive results.
But Gym Jones still raised the bar with 300 and again did exemplary work with Cavill on MOS. Shannon and Crowe's transformation was not nearly as important as Cavill's and for Cavill, they delivered.