From a character perspective, what I find interesting is that by sparing/not sparing Min, AJ is essentially choosing which of his parents to 'become' [in a philosophical sense]. Mohan.... was not a good man. He may have been a good fighter, but he was also increasingly consumed by his emotions, his hate. Before he killed Lakhsmana, he could have had everything he wanted for Kyrat: Min was on the path to reform, was hashing out a peace deal with the Golden Path, and had a stable influence in his life. All he had to do was give up Ishwari, and the idea that HIS path was the only one for Kyrat. But Mohan could not see beyond his own jealousy, his own path, and in one red moment ruined everything. If [in my view at least] AJ shoots Min, he is giving in to the same demons that destroyed his father [if on a level with smaller stakes, given the differing circumstances] and killing someone who doesn't, in the end, need to die because of his own rage. If, on the other-hand, he spares Min, he chooses the ideals of Ishwari [though her own path has problems]: he confronts the fact that killing Min won't really make anything better, that MOST of the killing he has done hasn't really made things better and.... lets go.
Things get more complex in the epilogue, when AJ is confronted by the actions of the GP leader he chose to support, and is given a choice to kill them. If you choose to kill them, AJ has ironically taken the same path Min has: things have moved full circle, and once again the [kinda]outsider has usurped the revolution and become king through murder. Now what? [The same problem exists in all spare-Min endings, since he technically abdicates in your favor, but choosing to kill your erstwhile allies after the revolution is so close to what Min did, that the Son of Mohan Ghale taking the same path as his greatest enemy is to deliciously ironic not to be intentional].
As for Ishwari, I always felt that she made the wrong choice by leaving, and her last request to her son is a final recognition of that fact. She was able to stabilize Min, and abdicating her role in Kyrat for her own reasons - regardless of how very valid they were - was a choice that had serious consequences.
As for Min, he - like Ishwari and Mohan, and all the others - knew that he could take a better path: there was no reason to become an artfully vicious despot after Lakshmana died: as he himself admits, he used it as an excuse. He knew the right thing to do, but did the wrong thing anyway.
There is a pattern here of characters seeing the right decision, knowing the best choices in their reach, , , but doing wrong anyway, and justifying it as best they can while everyone suffers. AJ is no different either: as Min correctly points out, he enjoyed playing the rebel far too much for it to simply be about obligation. However, he is given a second chance to do better than his predecessors. Does he take it? What happens then? That is for possible DLC to explore [or head-canon: in my mental ending, Sabal and Amita are both alive, part of a provisional government, and engrossed with AJ in the process of writing a new constitution that has bogged down in a dispute over water allocations for hydropower... I have an odd enjoyment for the minutae of politics].