SPOILERS!!

Yes, if it wasn't already clear from the title, SPOILERS! Anything you learn from this point on that you didn't want to know, is your own fault.

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Still with me? Ok, so, FarCry4's endings.
In true FarCry fashion, they try as hard as they can to make every decision you make as uncomfortable and unrewarding as possible. Despite all the dudes you kill, all the hoops you jump (wingsuit) through or whatever your intentions may indeed be, you always end up feeling like you made the wrong choice and just wasted your life doing all the wrong things. I guess that's just part of the franchise. One of the things I liked about FarCry2 was how it played on the reality that in almost all wars, there is no difference between the competing factions - the only winners are those who profit from the war itself and the losers are all those who fight and die for "the cause".
FC4 follows that same pattern by forcing you to choose between two "freedom fighters" who both feel they know what's best for their native country in the fight against the self-erected king, Pagan Min.

The game itself was quite fun for me overall. I never got around to playing FarCry3 (I wanted to, but that whiny, yuppy bitch you play as kept deterring me), so everything in FC4 is new to me. From what I've seen though, FC4 is to FC3 what New Vegas is to Fallout 3 - same assets in the same configuration, just with a different setting. Still, it was fun for me. Like with Shadow of Mordor, it's a great game to pick up, play for an hour or two, then go on to something else. It's also very fun to play in co-op - probably the first game for which I've admitted that. I could say more, but this journal is more about the endings then the gameplay.

---(Here is where the SPOILERS really start)---

The story for the most part is pretty backseat to the action and didn't really have any shockers, despite what I'm sure Ubisoft wanted to be a "twist" at the end.
You have two main protagonists to choose from, each one with some pretty obvious character flaws and some deep resentment of their rival, and from the very beginning it was obvious that once you go far enough with one, you'll end up having to kill the other. No surprise then when that happened.

I chose to side with Sabal for every single mission. Not because I had any particular loyalty to him, but because every mission where I was given a choice between the two, Amita's side just seemed less desirable. I wanted to like Amita, and I felt bad snubbing her every single time, but her desire to turn Kyrat into an opium and heroin manufacturer just seemed like more of a danger then Sabal's religious devotion.
Near the end, when (surprise surprise) Sabal sends you to kill her, I went ahead and let her live. Despite her fixation on creating a drug state, I felt that she honestly did want the best for the country, just in a very morally-devoid manner.
Sabal of course makes himself rather unlikable at the post-ending of the game (more on that later), but for the most part, I didn't have a problem with him. One of his first missions is to rescue some captives, while Amita wants you to save some intel instead. Personally, I felt that the lives of the captives were more important than the intel, even if a good argument could be made toward the other side. After that, pretty much every other mission is either saving a drug factory for Amita, or blowing it up for Sabal. For me, the choice was pretty easy. Drugs are bad, kids.

So I've scorned Amita at every turn, but spared her life at the end. Sabal is big man on campus and Pagan Min is still alive. A mission or two later (made way easier thanks to my penchant for doing all the side missions and unlocking all extra weapons before progressing the story), and I'm at Pagan's palace.
This is it. The final confrontation.
Pagan Min is not much of a villain. Vaas was a villain. He got off on torture and pain. He was psychotic and unambiguously evil. He ENJOYED being the bad guy and people enjoyed hating him; that made him memorable and really satisfying as a villain.
Pagan stabs someone early on in the game, but aside from that, he doesn't really do anything. Occasionally after main missions he will contact you through your walkie-talkie to lightly chide you about choosing the Golden Path or make smalltalk about your clothes or whatnot, but aside from that, he really is just a goal post that the game tells you that you eventually need to get to (the reason for his ambiguity toward the player becomes pretty obvious as you progress through the story).
Don't get me wrong, he's not a nice guy. But where Vaas was a psychotic killer who reveled in pain and bloodlust and sliding in the knife himself, Pagan just sits around checking the cut of his suit and having people executed with a blasé wave of his hand. He is the ambivalent head of a fanatic cult of personality, unconcerned about the people he lords over or the lives he throws away. He's basically a taller, thinner Kim Il-Sung. That alone makes him worth a bullet, but mostly on principle.

Eventually, after killing a lot of guys, reading a lot of journals and dealing with a lot of infighting, you get to confront Pagan himself and find out what the inevitable plot twist is.

>>SPOILERS AT CRITICAL MASS<<

>>EVACUATE JOURNAL UNLESS PREPARED TO DEAL WITH THE CONSEQUENCES<<

>>DON'T SAY I DIDN'T WARN YOU<<

My initial theory was that Pagan Min was actually Arjay's father, not Mohan Ghale (it's already obvious by that point in the game that Ishwari had come to love Pagan more than Mohan), but it turns out I was only half right. Mohan Ghale and his wife, Ishwari, fought regarding her role in the future of Kyrat and the path Mohan was taking. Mohan eventually sends Ishwari to Pagan, planning to have her spy on him and send information back to the Golden Path. She instead falls in love with him and conceives his illegitimate child - Lakshmana - the player's half-sister. Your mother's wish to have her ashes laid to rest with Lakshmana is her desire to be reunited with her daughter.
According to Pagan, Mohan killed Laksmana out of jealousy, and Ishwari killed Mohan before fleeing to America. He then insinuates that Ishwari's departure and the death of his daughter is what changed him into "this". If I was suppose to feel sympathetic for him, I missed my chance. From the notes and journals you read, Pagan was already a nasty and untrustworthy person BEFORE he had ever met Ishwari - arguably even moreso.
He was the son of a Chinese drug lord, who upon inheriting his father's modest empire, decided that his share of the trade was too small compared to the established rivals in China, but was more than sufficient to outreach elsewhere.
He allied himself with Royalist forces in Kyrat, who were trying to reinstate the monarchy after a coup. They accepted his aid gladly, as Pagan's private army was better trained and better equipped than the junta forces set up after the coup. Once victory was achieved, Pagan assassinated the royal heir and set himself up as king, killing off all those who resisted. Mass killings and the rapid installment of opium fields and heroin factories alongside epitomous posters and propaganda declaring Pagan to be godlike and worshipful.
The fact that he fell in love and lost a daughter to someone he betrayed is not enough to make me feel any form of sympathy for him. Nor does it excuse his continued actions as the ambivalently callous ruler of a despotic regime. So, yes, I have no love at all for Pagan Min.
So when I walked into his dining room, after listening to him prattle about "which Arjay" he was talking to, I put a bullet in his neck as soon as I was given control. That apparently is the BAD ending.
If you sit and listen to Pagan, he explains the love affair between himself and Ishwari (which you should already know about) and reveals that Laksmana is your half-sister. He ushers you into the shrine holding Laksmana so you can place Ishwari's ashes alongside her. When you come back out, Pagan leaves you as the new king of Kyrat and then flies off in his helicopter. That, is the GOOD ending.

There is actually one other ending, according to developers. As Pagan is leaving on his helicopter, if you're quick, you can still shoot him down. You get the "King is Dead" achievement and can go down to the wreck where you can loot Pagan's corpse. He has two unique items, a pin and the pen he used to stab the guard in the opening cutscene. Apparently that is the first step, but as far as I know, no one has figured out the rest yet.

Unfortunately, there appears to be no way to go back and replay the final mission. The game has no alternate save files, and if I were to try and restart the game, I would go back to square 1 with no way of reloading my previous save (it can be done using a bit of a crack, but you shouldn't have to hack the game for something so simple). Considering how many endings there are, and how much extra stuff there is in the game, that's just a crime.

But there you have it - the GOOD ending is to allow the dictator to escape just because he loved someone once. Maybe it's just a representation of how jaded I am in my elder years ( :-P ) but that doesn't sit too well with me. I knew moments after the start that the game would try and make Pagan sympathetic, so that killing him became a moral challenge, but this wasn't really it. He was not a good guy, never became a good guy and I had no reason to expect him to become a good guy in the future. He was a dick his whole life and that's a hard pattern to break. Revealing to me that the father I never knew may have been a dick, or that Pagan had the hots for my mother and gave he a half-sister I never knew do not wipe away the myriad of crimes for which Pagan is clearly responsible.
And, simplistic as it may be, killing Pagan straight out and saving Ajay from that revelation...well, ignorance is bliss.