My conclusion was that there were no "good guys", including Pagan Min.
Too bad Ubi didn't offer up a scenario similar to FC2 - there are no "friendlies" in Kyrat in the civil war, and Ajay's only mission(s) was to determine how to actually deliver his Mom's ashes to "Lakshmana".
"The NUKE, are you crazy?" "Oh relax, it's got a very small yield. Just enough ..."
IMO the most satisfying game ending is the one where you don't even play the game - just wait for Pagan Min to return at the start of the game and he shows you to Lakshmana's shrine. Other endings left me feeling slightly disappointed. I agree with Mike - definitely no good guys in this game.
Yeah no good guys Then again this IS a Far Cry game where there are no black and white moral choices (or darn few anyway)
If you read everything you can see how Mohan is painted in a different light and Ajay's mom's relationship with Pagan is not so simple as we are first led to believe.
Having suffered through real loss in my life I feel like I can now identify more with Pagan's pain. Why he may have been driven to extremes. I think some people are truly just 1 tragedy away from becoming supervillians
...But that is just "sympathy for the devil". We must not lose sight that while Pagan does not personal harm Ajay and even appears friendly and possibly loving - he still has caused MUCH harm to others.
He knows, approves of and encourages Paul Depleurs torture methods. He destroyed Noore's life (who runs the arena) in a profoundly horrible way. God knows the horrors he inflicted on the "common" people of Kyrat. Heck it may have been a twisted joke but by his own admission he kidnapped and/or killed a celebrity chef's family. He is... not a very nice man...
Stumbled across this which talks about a lot of these things:
Overall I think Pagan was a great villain, BECAUSE it's harder to dislike him. I do give credit to the devs for doing a great job with that. I only wish they would have made Ajay less... uninteresting. I guess the thought was if Ajay has no real reactions to any of this it will not mentally sway your opinions one way or the other allowing the players to decide themselves what to think about Kyrat and it's "leaders".
Spoiler Alert** Agreed there's either no good guys or you can pick either to be the good guy, except Sabal. For me the story in FC4 is the best by far. I'd still pay for a FC4.x where you could choose to side with Pagan or continue the game to take over the country as Pagan mentions. It would be good to see a change in the Kyrat Army, once Pagan turns the country over to you. (He should have let someone else know about that, if it was your country from the beginning)
Also - If he survives the story could pick up there also, him to another country that used to be a part of Kyrat. (Or partnering with him)